tag:blogger.com,1999:blog-47185770883437792462015-04-01T10:16:18.415+13:00The AtavismDavid Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.comBlogger229125tag:blogger.com,1999:blog-4718577088343779246.post-11839352339287348362014-01-26T16:49:00.000+13:002014-01-26T16:49:51.071+13:00A Very Special edition of Sunday Spinelessness<div class="separator" style="clear: both; text-align: left;">
Wow, it's been a long time since I wrote something here. Let's see if I can remember how this goes: I find a weird-looking bug and take some photos. Then I enthuse about that bug for a few paragraphs, hoping some broader point will emerge from all my geekery..</div>
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All right then, here's a neat creature I found recently in the Wellington Botanic Garderns. It's <i>Helpis minitabunda </i>the Australian Bronze Jumping Spider:</div>
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<a href="http://3.bp.blogspot.com/-ouHXEsRL5BU/UuRaPp3xg7I/AAAAAAAAS_Y/57vKB1WbsPc/s1600/Ana+%2526+David.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-ouHXEsRL5BU/UuRaPp3xg7I/AAAAAAAAS_Y/57vKB1WbsPc/s1600/Ana+%2526+David.jpg" width="550" /></a></div>
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OK, so just this once the vertebrates might be the most interesting things in these photos. In November Ana, who has for many years put up with me turning over leaves and rolling rocks in search of interesting critters, and I got married. Since Ana made the most beautiful bride, and we had a wonderful day in the Botanic Gardens I can't help but share a few more photos:</div>
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<a href="http://4.bp.blogspot.com/-fVuzt0vhynA/UuRaQJCO7TI/AAAAAAAAS_c/02lIrl9g6BE/s1600/Ana+%2526+David1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-fVuzt0vhynA/UuRaQJCO7TI/AAAAAAAAS_c/02lIrl9g6BE/s1600/Ana+%2526+David1.jpg" width="550" /></a></div>
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Since getting married Ana and I have set out on another adventure. We've moved from the green and pleasant land in those photos to the endless sun and aridity of the Sonoran desert:</div>
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<a href="http://3.bp.blogspot.com/-GXBD3t_GB-g/UuSBF2nTLRI/AAAAAAAAS_4/GAa1YPfsxRA/s1600/Downloads.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-GXBD3t_GB-g/UuSBF2nTLRI/AAAAAAAAS_4/GAa1YPfsxRA/s1600/Downloads.jpg" width="550" /></a></div>
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I am a doing a postdoc with <a href="http://cartwrig.ht/lab/">Reed Cartwright</a> at Arizona State University, where <a href="http://pandasthumb.org/archives/2013/06/postdoc-positio.html">I am working to develop new techniques for detecting mutations from sequencing data and applying those methods to a very cool experiment&nbsp;</a>.</div>
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Ana and I are starting to settle in to &nbsp;life here in the desert (I don't think we'll really be integrated into Phoenician life until we have a car, but that will happen soon), so I hope <i>The Atavism</i>&nbsp;will spring back to life soon. There certainly shouldn't be a shortage of topics to cover - I have a whole new invertebrate fauna to nerd out over, &nbsp;life in the desert to learn about and a whole new science system to try and understand!</div>
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<br />David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com3tag:blogger.com,1999:blog-4718577088343779246.post-47891092838974384292013-06-17T17:30:00.000+12:002013-06-17T19:18:02.423+12:00Sequencing the tuatara genomeThings have been quite around here for a while. Largely for the typical boring reasons, the pressure to get work done and on to journals that might publish it&nbsp;leaving&nbsp;little spare time. On top of that the non-science time I've had lately has taken up by what I think will be a &nbsp;very important piece of science communication: <a href="http://sciblogs.co.nz/tuataragenome/2013/06/17/why-sequence-the-tuatara-genome/">a blog documenting The Tuatara Genome Poject.</a><br />
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I'll keep trying to find time to share my&nbsp;thoughts&nbsp;here, but I really encourage all my readers to read and follow the tuatara blog - we're going to be discussing everything from why we'd want &nbsp;to sequence a genome, to&nbsp;actual&nbsp;process we'll use to it and some of the results that we'll gather. I won't be writing every word, in fact, one of the goals is to get the researchers on the project to describe their work in their own words. Hopefully we'll all learn a bit about reptiles, genome sequencing bioinformatics and a whole lot more.David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-23815244973542019872013-02-17T13:43:00.000+13:002013-02-19T09:46:22.909+13:00Sunday Spinelessness - Mostly True Facts about land snailsThe ailing laptop on which I write these posts has developed a new symptom - a non-deterministic&nbsp;keyboard. So, I hope you'll excuse me if I just paste a link and get on with something less annoying than trying to write a post via a cellphone.<br />
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It's a pretty good link too.&nbsp;<a href="https://www.youtube.com/user/zefrank1">Ze Frank</a>'s "True Facts" series of zoological oddities has finally got to the best&nbsp;creatures&nbsp;on earth, land snails:<br />
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<iframe allowfullscreen="" frameborder="0" height="315" src="http://www.youtube.com/embed/VTV23B5gBsQ" width="550"></iframe><br />
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Pretty much everything Frank says about snail mating is true so, laptop&nbsp;permitting, I'll use next week's post to expand on how&nbsp;anatomy&nbsp;and&nbsp;behaviour&nbsp;have co-evolved&nbsp;&nbsp;to give us produce these mating habits, and how they effect evolutionary processes in land snail populations.David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com1tag:blogger.com,1999:blog-4718577088343779246.post-4131697949127494862013-02-12T12:18:00.000+13:002013-02-12T17:01:07.034+13:00Darwin and New ZealandFebruary the 12th is the <a href="http://darwinday.org/">anniversary of Charles Darwin's birth.</a><br />
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Across the world people will be marking the day by remembering Darwin the discoverer of evolution by natural selection, <a href="http://sciblogs.co.nz/the-atavism/2010/02/12/charles-darwin-and-the-origin-of-spouses/">Darwin the cautious husband</a>,&nbsp;Darwin the barnacle boffin and maybe even Darwin <a href="http://darwin-online.org.uk/EditorialIntroductions/Chancellor_CoralReefs.html">the geologist who explained the origin of coral atolls</a>. I might be the only person who takes some time today to remember Darwin as a grumpy young traveler.<br />
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Darwin in New Zealand</h3>
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Darwin visited New Zealand in 1835, and he really didn't like it.The New Zealand visit came four years into the HMS <i>Beagle</i>'s voyage, and at the end of a four thousand kilometer journey from Tahiti. Darwin and the Beagle's crew had loved their time in Tahiti (Darwin records that "every voyager ... offered up his tribute of admiration" to the island <a href="http://darwin-online.org.uk/content/frameset?pageseq=429&amp;itemID=F14&amp;viewtype=side">p 416</a>). With the memory of Tahiti in mind, the sight of fern-clad hills, a few European houses and a single waka to act as a greeting party was a disappointment for Darwin:<br />
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Only a single canoe came alongside. This, and the aspect of the whole
scene, afforded a remarkable, and not very pleasing contrast, with our
joyful and boisterous welcome at Tahiti. (<a href="http://darwin-online.org.uk/content/frameset?pageseq=430&amp;itemID=F14&amp;viewtype=side">p 417</a>)
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Closer inspection of the land around the Beagle's mooring in the Bay of Islands didn't do much to improve the young Darwin's opinion of New Zealand<br />
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In the morning I went out walking; but I soon found that the country was
very impracticable. All the hills are thickly covered with tall fern,
together with a low bush which grows like a cypress; and very little
ground has been cleared or cultivated .. (<a href="http://darwin-online.org.uk/content/frameset?pageseq=431&amp;itemID=F14&amp;viewtype=side">p 418</a>)</blockquote>
And if the plants weren't enough,&nbsp; introduced predators had already removed much of native fauna: <br />
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I saw very few birds.. It is said that
the common Norway rat, in the short space of two years, annihilated in
this northern end of the island, the New Zealand species. In many places
I noticed several sorts of weeds, which, like the rats, I was forced to
own as countrymen. (pp <a href="http://darwin-online.org.uk/content/frameset?pageseq=440&amp;itemID=F14&amp;viewtype=side">427-8</a>)</blockquote>
In nine days of traveling around the Bay of Islands Darwin found very little to like. In comparison to the Tahitians the Māori were "of a much lower order" (<a href="http://darwin-online.org.uk/content/contentblock?itemID=F14&amp;basepage=1&amp;hitpage=430&amp;viewtype=side#">p 420</a>) and the Europeans inhabitants where "the very refuse of society" (<a href="http://darwin-online.org.uk/content/contentblock?itemID=F14&amp;basepage=1&amp;hitpage=430&amp;viewtype=side#">p 420</a>). In fact, the only place he liked was <a href="http://en.wikipedia.org/wiki/William_Williams_%28bishop%29">William Williams</a>' attempt to remake England at the Mission house in Waimate North. (<a href="http://darwin-online.org.uk/content/frameset?pageseq=438&amp;itemID=F14&amp;viewtype=side">pp 425-30</a>).<br />
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Now, it is obvious that Darwin meet New Zealand at a bad time. The capital, Kororareka, had well and truly earned its nickname as the "Hell Hole of the Pacific", Maori where adjusting to life alongside Europeans, and the impact of the <a href="http://en.wikipedia.org/wiki/Musket_Wars">Musket Wars</a> and the native flora and fauna was already in decline thanks to the introduction of pests and the clearing of forests. But when you consider that Darwin was in the <i>Bay of Islands</i> in <i>summer time </i>I don't think I'm being too parochial&nbsp; to suggest Darwin was being just a tad grumpy when he decided there was nothing to like in our country:<br />
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<span style="font-size: x-small;">Left: <a href="http://www.flickr.com/photos/fras/3621128285/sizes/m/in/photostream/">Pahia beach,</a> <a href="http://creativecommons.org/licenses/by-nc-nd/2.0/">CC 2.0 </a>by <a href="http://www.flickr.com/photos/fras">Fras1997 </a>. Right: <a href="http://www.flickr.com/photos/chris_gin/8264199681/">Tapeka Sunrise</a>, <a href="http://creativecommons.org/licenses/by-nc-nd/2.0/">CC2.0 </a>by <a href="http://www.flickr.com/photos/chris_gin/">Chris Gin</a></span></div>
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New Zealand in Darwin's thinking</h3>
Darwin didn't think much of New Zealand while he was here, but I suspect he ended up regretting the brevity of his visit. About 30 years after he gladly left our islands behind, Darwin <a href="http://www.darwinproject.ac.uk/entry-4245">wrote a letter</a> to <a href="http://www.teara.govt.nz/en/biographies/1h1/haast-johann-franz-julius-von">Julius Von Haast</a> to thank him for some information he'd provided, adding<br />
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<a class="footnoteLink" href="http://www.darwinproject.ac.uk/entry-4245#mark-4245.f8" name="back-mark-4245.f8" title="4245.f8"></a> I really think there is hardly a point in the world so interesting with respect to geographical distribution as New Zealand</blockquote>
Darwin spent a lot of time thinking about&nbsp; the geographical distribution of species. His first written account of where species might come from was spurred by thinking abut the distribution of Galapagos and Ecuadorian mockingbirds*. More importantly, if Darwin was going to do away with the popular idea that each continent's species arose more or less in their current place, he had to work out how plants and animals could get from one place to another.<br />
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He developed contacts in New Zealand and his correspondence with other scientists has many references to our plants and animals. The presence of flightless birds, bats and the effects of glaciation all come up multiple times. But New Zealand's most important influence on Darwin's thinking came via his best friend, <a href="http://en.wikipedia.org/wiki/Joseph_Dalton_Hooker">Joseph Hooker </a>.<br />
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Like Darwin, and many other Victorian naturalists, Hooker started his career by jumping on a ship and sailing to the other side of the world. For Hooker, that meant the HMS <i>Erebus</i> and trip to Antarctica via South America, New Zealand and Australia. Hooker had read Darwin's <i>Journey of the Beagle</i> in proof before he set off, and when he returned to England the two stayed in contact.<br />
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In 1844 Darwin "<a href="http://www.darwinproject.ac.uk/entry-729">confessed</a>" his ideas about the origin of species to Hooker. That letter contains references to the New Zealand flora, in which Darwin is fishing for facts that might support his ideas about species moving from one land to another. In the same year, Darwin started a discussion with Hooker about the distribution of Kōwhai (<a href="http://en.wikipedia.org/wiki/Sophora"><i>Sophora</i></a>). The yellow-flowering Kōwhai will be familiar to all New Zealanders, but it may come as surprise that some of the "Kōwhai" species sold in garden centres aren't from New Zealand at all, but are Chilean <i>Sophora</i> species. The species are similar enough they'll happily hybridise given the chance.<br />
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These Chilean Kōwhai are an example of a common pattern - the floras of New Zealand, Tasmania South American and the sub-Antarctic seem to be closely related. Hooker thought this pattern arose because all these island where connected in a southern super continent. Darwin didn't like the idea of creating new land to explain a biological pattern, and instead proposed that that chance dispersal (by wind or rafting) could explain the distrbution of these species. Darwin was a keen experimentalists, and so, he set about dropping seeds in salty water and attempting to germinate them. These experiments took place in Darwin's house in Down, and apparently his children counted each germination <a href="http://www.darwinproject.ac.uk/entry-1671">as a victory for their dad over Hooker</a>.<br />
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It seems Hooker couldn't provide Kōwhai seeds for Darwin's experiments, but <a href="http://www.darwinproject.ac.uk/entry-4921">Darwin took a record of just three equally-sized Kōwhai trees on the Chatham Islands (some seven hundred kilometers from the mainland) as evidence for long-range dispersal</a>, and perhaps a suggestion that Kōwhai seed could survive a trip from Chile to New Zealand.<br />
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It turns out Darwin was right about <a href="http://www.darwinproject.ac.uk/entry-4921">Kōwhai&nbsp;</a> although he got the direction wrong. Molecular studies have shown that <i>Sophora </i>arose in the Northern Pacfic, dispersed down to New Zealand and arrived in Chile via the Antarctic's strong circumpolar current, all in the last few million years (Hurr et al, 1999 doi: <a href="http://dx.doi.org/10.1046/j.1365-2699.1999.00302.x">10.1046/j.1365-2699.1999.00302.x</a>).<br />
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Honouring Darwin Day in New Zealand</h3>
I'm not quite sure how I feel about Darwin Day. There is not doubt that Darwin was a genius, an exellent naturalist and the founder of a field of study that lives on today. But there is something a bit odd about the annual veneration of Darwin, and the rush to connect modern ideas in evolutionary biology with things Darwin wrote 150 years ago.<br />
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Darwin got a lot right, and foresaw many developments in the study of evolution. But evolutionary biology is much more than 21st century 'Darwinism'. Darwin didn't know what a gene was, so is unlikely to teach us much about genomics. For me, the most important thing to learn from Darwin's writing is the way he set out about understanding the world. Darwin sought out evidence for each sub-hypothesis in his Big Idea, sometimes that meant writing to colleagues like Hooker and Haast and sometimes that meant doing experiments like his salty seeds.<br />
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Darwin never got a Kōwhai seed to experiment with, but, in his 1958 lecture on <a href="http://rsnz.natlib.govt.nz/volume/rsnz_86/rsnz_86_03_004350.html">Darwinism in New Zealand</a>, AC Flemming mentioned a study that found they can survive 4 months of immersion in salt water. That's a little shorter than the time you'd expect a seed pod set adrift from New Zealand to take before it washed up on a Chilean beach. Right now, highschool students are starting another year of biology classes - and teachers are probably preparing another re-hash of the "plant study" they've taught to Year 13 students since they were called Seventh Formers. Wouldn't it be a fitting tribute if some of those classes did something a little different, and honoured Darwin's approach to undestanding the biological world by dunking Kōwhai&nbsp; seeds and running an experiemnt he never got to?<br />
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Quoted passages are from Darwin's <i>Voyage of the Beagle. </i>Links go the the <a href="http://darwin-online.org.uk/content/frameset?pageseq=440&amp;itemID=F14&amp;viewtype=side">Darwin Online Fascimile</a>. <br />
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*<a href="http://www.nhm.ac.uk/about-us/news/2008/november/darwins-mockingbirds-knock-finches-off-perch23090.html">Forget about the finches</a><br />
<br />David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com1tag:blogger.com,1999:blog-4718577088343779246.post-36395212684617915172013-02-03T19:51:00.000+13:002013-02-03T19:51:57.069+13:00Sunday Spinelessness - Cannibalism in the gardenThe most common jumping spider in our garden, <i style="font-style: italic;">Trite auricoma, </i>with the remains of it most recent meal... a smaller&nbsp;<i>T. auricoma:</i> <br />
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Cannibalism,&nbsp;&nbsp;animals eating members of their own species, is a pretty common and widespread&nbsp;behavior. Species in almost every phylum have been shown to&nbsp;occasionally (or frequently) eat members of their own&nbsp;species.&nbsp;Even&nbsp;herbivores&nbsp;like&nbsp;monarch butterfly&nbsp;caterpillars&nbsp;will eat any monarch eggs they encounter.<br />
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In spiders, the most well-studied form of&nbsp;cannibalism relates to mating. In&nbsp;a very&nbsp;few species male spiders will offer themselves as a meal to their mate. In so doing, males make sure&nbsp;their offspring get the best start in life, by providing their mother with a&nbsp;nutrition&nbsp;meal. They are often also posthumously rewarded by female, who reject other suitors and ensure the&nbsp;sacrificial&nbsp;male's legacy.&nbsp;The best example of this behaviour comes from the Australian red back spider (<i>Latrodectus hasseltii). I</i>n this species males&nbsp;actually pirouette their way into their mate's fangs, and females take up the offer about 65% of the time. New Zealand's endemic red back relative, <a href="http://sciblogs.co.nz/the-atavism/2010/06/13/sunday-spinelessness-protecting-the-katipo/">the katipo</a>, does not exhibit this&nbsp;behavior&nbsp;(nor does the North American black widow, despite the name).<br />
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Such sexual cannibalism isn't known from jumping spiders (although females will certainly eat unwary males), and a wider (and earlier) shot lets you see that this was a case of a mature spider taking a younger one (males and females are about equally sized in <i>T</i>.&nbsp;<i>auricoma</i>).<br />
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<i><i><br /></i></i>David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com1tag:blogger.com,1999:blog-4718577088343779246.post-33186681833399354642013-01-31T12:46:00.000+13:002013-01-31T12:46:13.281+13:00ElsewhereA couple of links that might be of interest for readers of <i>The Atavism:</i><br />
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<li>I've&nbsp; been really remiss in<a href="http://www.radionz.co.nz/national/programmes/ourchangingworld/20121206"> linking to interview I did with Veronika Meduna for Radio NZ's Our Changing World</a>. The bugs Veronika and I visited will all be familiar to readers here</li>
<li>&nbsp;The online<a href="https://evobiojournalclub.wordpress.com/"> Evolutionary&nbsp; Biology Journal Club</a> is getting back together for "Season 2". If you don't know, a<a href="http://en.wikipedia.org/wiki/Journal_club"> journal club</a> is basically a bunch of geeks getting together to discuss recent (or no so recent) papers in a shared area of geekiness. As the first paper in this season's line up is one I already know pretty well&nbsp; <a href="https://evobiojournalclub.wordpress.com/2013/01/30/paper-summary-de-queiroz-1998/">I wrote a quick summary of it </a>to serve as a jumping-off point. The discussion will be on Tuesday morning NZ time, and anyone who is keen can jump in (and if next week doesn't work there will be plenty more sessions this year).</li>
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David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-17299385340276785322013-01-27T21:36:00.000+13:002013-01-27T21:36:02.022+13:00Sunday Spinelessness - Native bees againLast year, at about this time, I wrote a little about our <a href="http://sciblogs.co.nz/the-atavism/2012/01/29/sunday-spinelessness-we-have-bees/">native bees</a>. Though I'm glad to have done my little bit to promote the existence of these all too anonymous members of our natural&nbsp;heritage&nbsp; I've always felt a little&nbsp;embarrassed&nbsp;by the photos in that post.&nbsp;As I admitted at the time the photos are staged. Photographing our twitchy little bees is hard - apart from being small, they zip about from flower to flower much more quickly than I can line up, let alone focus, shots.<br />
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So, to illustrate the original post I used half-drowned bees, scooped out from a swimming pool. The time it took the bees to dry out gave me a chance to take the photos, but I set them up on <i>exactly </i>the type of flower they'd never visit in the wild. So, not only did I cheat, but the photos I took actively misled about the true nature of bees!<br />
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So, here are some much worse photographs of native bees that do a much better job of representing their lifestyles. First off, a bee&nbsp;perched on a favourite&nbsp;flower, a <a href="http://en.wikipedia.org/wiki/Hebe_(genus)">hebe</a>, &nbsp;and deciding on its next move:<br />
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and another collecting pollen from the same plant:<img src="https://lh5.googleusercontent.com/-k5aQEvMKQFI/UQTikCbg98I/AAAAAAAASCo/CJstZY543DE/s550/polinating.JPG" />
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These hebes, and a few parsley plants left to go to flower, make my parent's house in the Wairarapa a mecca for native bees. They certainly make their mark around the garden, if you don't notice them drowned in the pool or visiting flowers you can see their nests in the soil:</div>
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David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-18400287736458800842013-01-22T15:36:00.000+13:002013-01-22T20:22:50.922+13:00Cats aren't evil, but they are a problem<div style="text-align: center;">
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<a href="http://garethsworld.com/catstogo/">It seems Gareth Morgan has declared a war on cats</a>. It will, I'm sure, come as a great surprise to you that Morgan's description of cats as ruthless and sadistic killers that we must eventually purge from the land&nbsp; has met some opposition. Invoking outrage is pretty good way to get free advertising in New Zealand, and if you measure the campaign's success in<a href="http://www.listener.co.nz/commentary/the-internaut/faster-pussycat-kill-kill/"> tweets, comments and talkback calls</a> I guess Morgan is on to a winner. But I'd like to think we can do better than simply setting up an argument between supporters of Morgan's <a href="http://en.wikipedia.org/wiki/Four_Pests_Campaign">Maoist </a>purge and cat lovers who think their moggie can do no harm.<br />
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Cats are a problem</h3>
Most of the reaction to Morgan's campaign has been to basically treat it as a joke. We should be clear then, that introduced predators are the number one threat to New Zealand species. Stoats, weasels possums and rats all contribute the decline of birds and lizards (and invertebrates, though we don't monitor those species closely enough to track their progress). Cats are certainly part of that problem. They have contributed to the extinction of at least 6 bird species&nbsp; in New Zealand, and many more populations and subspecies have been lost partly as a result of predation by cats (Merton, 1978). Cats continue to pose a threat to our wildlife. The impact of feral cats on shorebirds&nbsp; (plovers, dotterels, oystercatchers) and kakapo is well documented (Karl and Best, 1981 doi: <a href="http://dx.doi.org/10.1080/03014223.1982.10423857">10.1080/03014223.1982.10423857</a>). In the space of a week <a href="http://www.doc.govt.nz/about-doc/news/media-releases/2010/cat-nabbed-raiding-the-mothership/">one cat managed to kill 102 native short tailed bats</a>.<br />
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The problem isn't restricted to wild cats. Pet cats will attack and kill native birds and lizards when they have the chance. In Dunedin the impact of tame cats is large enough that it's been estimated local bird populations (including natives) wouldn't survive if they weren't replenished by migrants from around the fringes of the city (van Heezik, et al. 2010. doi: <a href="http://dx.doi.org/10.1016/j.biocon.2009.09.01">10.1016/j.biocon.2009.09.01</a>)<br />
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</a>Getting rid of cats isn't necessarily a solution</h3>
It's clear then, that cats are a problem for the conservation of native wildlife. But it's not nearly as clear that simply getting rid of cats will be much help. Every study of the diet of cats in New Zealand has found that cats kill a lot of mice and rats. These rodents are themselves predators of birds so removing one predator from our country <a href="http://en.wikipedia.org/wiki/Mesopredator_release_hypothesis">may simply let another run amok</a>. When feral cats were removed from Little Barrier island it led to an outbreak in kiore (Pacific rat), which threatened Cook's Petrel populations on that island (Rayner et al, 2007 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409232/">avaliable via PMC </a>).<br />
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Should we phase out cats in New Zealand?<br />
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So, if Morgan's plan was actually do-able, should we do it? I have to honest here and tell you, I don't know. It's abundantly clear that cats, both feral and domestic, can kill native animals. It's clear that in at least some cases that killing can have a major impact on populations, but removing cats might not help all that much. If you want to know whether the impact of your typical urban moggy justifies Morgan's campaign, especially given the abundance of rats in New Zealand, you'd have to ask a conservation biologist. That's something no news organization has bothered with yet, as far as I can tell.<br />
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Is this the conversation we should have started?</h3>
It's fairly obvious that Morgan's website, with its strange anthropomorphism (cats are predators sure, sadists? no) was designed to draw headlines and "start conversations". But what hope is there for environmentalists in conversation where our side wants to take people's kittens away?<br />
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Introduced predators are the biggest threat to New Zealand's biodiversity, so the goal of eventually controlling these predators so tightly that they no longer pose a threat is a very worthy one. But the sort of change required to get us from today, where only 12% of the conservation estate is managed for predators, to that goal <i>has</i> to come from the ground up. Picking fights like this will get you headlines, but I don't think it will change anyone's mind.<br />
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Merton, Donald V. "Controlling introduced predators and competitors on islands" pp 121-128. In Temple, S.A. (ed.) <i>Endangered birds: management techniques for preserving threatened species</i> 1978<br />
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(image at the top via Pauline Dawson/<a href="https://twitter.com/Artandmylife">ArtAndMyLife)</a> <br />
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David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com35tag:blogger.com,1999:blog-4718577088343779246.post-72289122969284222592013-01-20T20:35:00.001+13:002013-01-21T09:19:26.526+13:00Sunday Spinelessness - 5 down.... quite a few to goI got some good news this week - a paper I'm an author on was accepted for publication pending some minor revisions. That's great because career advacement in academia rests largely on what we publish, and this is a good paper that I'll be happy to add to my CV. It's also quite happy about his particular paper being (almost) accepted because it's about <a href="http://en.wikipedia.org/wiki/Serpulidae">serpulid</a>s, segmented worms of the phylum Annelida (relatives of earthworms). A new phylum for me.<br />
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Biology is about diversity. I know I always go on about this, and end up affecting the overly-enthusiastic style of the guide in Douglas Adams's<i> Hitchiker's Guide to the Universe</i>: <br />
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Biological is diverse. You just won't believe how vastly, hugely, mind- bogglingly diverse it is. I mean, you might think there are lot of creatures in your average David Attenborough documentary, but that's just peanuts to the true diversity of biological systems, listen...</blockquote>
Well, I don't know to put in words, so let's try a picture. All that biological diversity got here because life evolves. When populations&nbsp;break up&nbsp;they are free to evolve apart from each other and develop entirely new functions or features and so become different. In this way, life is a tree, forming new branches as populations split. When we come to deal with the diversity of life, biologists try to reconstruct that tree, giving names to those tips and twigs which belong to a particular branch. In that&nbsp;&nbsp;<a href="http://en.wikipedia.org/wiki/Linnaean_taxonomy">system of classification</a>&nbsp;the&nbsp;phylum (plura phyla) is the one of the deepest&nbsp;divisions.<br />
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&nbsp;Creatures in&nbsp;separate&nbsp;phyla have usually been evolving apart from each other for 600 million years or more, and represent entirely different ways to deal with the trials of life. The annelid paper will mean I've published on 5 different phyla. That's exciting for me - it's nice to think I've added a little to our knowledge of decent sampling of the tree of life. But the truth is, biology is just so diverse that I've not even made a dent the tree of life. Here's a picture of all the Eukaryotic phyla (that is, creatures with cells like ours, but not bacteria and&nbsp;<a href="http://en.wikipedia.org/wiki/Archaea">archaea</a>) with only those I've published at least one paper on&nbsp;labeled:<br />
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Tree was drawn and shaded with <a href="http://itol.embl.de/">iTOL</a>'s nifty interfact to <a href="http://itol.embl.de/other_trees.shtml">the NCBI taxonomy</a>. There's a couple of things to note here. Because this is the NCBI taxonomy it's&nbsp;a curated tree rather than the result of any particular analysis. Although we aim to create biological groups "natural", in the sense they are a single branch in the tree of life, the rank giving to a particular branch is somewhat&nbsp;arbitrary&nbsp;and will differ between different groups (so green plants, which&nbsp;traditionally&nbsp;had "divisions" &nbsp;rather than phyla are certainly underrepresented here). Protists (single-celled eukaryotes) are certainly diverse, but <a href="http://skepticwonder.fieldofscience.com/">Psi Wavefunction</a> tells me protistologists have almost given up on rank-based taxonomy so this might not be a fair representation of them.</div>
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In any case, it's certainly a spur to me to get back to work and fill in a few blanks on the figure!</div>
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David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-2185398350400066622013-01-13T13:01:00.000+13:002013-01-13T13:01:10.447+13:00Sunday Spineless - On the WingJust a photo today, but a pretty awesome one I reckon. An inbound bumble bee from my parents' garden in the Wairarapa:<br />
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(~50 out of focus shots from same session not shown!)</div>
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David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-37393031785743865962012-12-09T22:29:00.001+13:002012-12-09T22:29:11.873+13:00Sunday Spinelessness - A Clearwing mothAt last, Dunedin has managed to arrange a proper summer day for a weekend.<br />
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The extra heat and sun saw plenty of bugs out and about, and I spotted plenty of familiar critters (native bees, &nbsp;cicadas, drone flies and magpie moths)&nbsp;for this first time this year. &nbsp;The real find of the weekend though, was something entirely new to me:</div>
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You might be a little&nbsp;surprised&nbsp;to learn that you are looking at a moth.<br />
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I'm helping design an undergraduate lab on&nbsp;systematics and taxonomy&nbsp;at the moment. &nbsp;Since the new lab is about insects I've suddenly become very aware of the traits that distinguish various insect groups. &nbsp;Moths, along with butterflies, make up the order Lepidoptera. You can see a few lepitoperan characters in the above photo: a mouth&nbsp;designed&nbsp;for siphoning nectar from flowers and a body covered in fine scales.<br />
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"Lepitoptera" actually mans "scaley wing", and, indeed most butterflies and moths have scales on their wings. This species, though, has got rid of most of it's wing scales (there are plenty of scales on the&nbsp;trialing&nbsp;edge though):<br />
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<i>Synanthedon tipuliformis</i> * is member of the "clear wing" moth family Sesiidae. Although I think this one is pretty neat, the family contains some&nbsp;striking species, the most interesting of which are&nbsp;wasp-mimics</div>
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<i style="background-color: #f9f9f9; font-family: sans-serif; font-size: 12px; line-height: 19.200000762939453px; text-align: start;"><a class="extiw" href="http://en.wikipedia.org/wiki/en:Bembecia_ichneumoniformis" style="background-image: none; color: #663366;" title="w:en:Bembecia ichneumoniformis">Bembecia ichneumoniformis</a></i><span style="background-color: #f9f9f9; font-family: sans-serif; font-size: 12px; line-height: 19.200000762939453px; text-align: start;">&nbsp;</span><span style="background-color: #f9f9f9; text-align: start;"><span style="font-size: x-small;"><span style="font-family: sans-serif;"><span style="line-height: 19.196969985961914px;">photographed</span><span style="line-height: 19.200000762939453px;">&nbsp;by <a href="http://en.wikipedia.org/wiki/File:Bembecia_Ichneumoniformis_FemelleMorgat2011Lamiot993.jpg">Lamois</a> and licensed <a href="http://creativecommons.org/licenses/by-sa/3.0/deed.en">CC3.0</a></span></span></span></span></div>
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Yes, that's a moth! Sesis apiformis <a href="http://www.flickr.com/photos/26522217@N00/3690358997">from Flickr user Oldbilluk</a>. Licensed <a href="http://cc2.0http//farm3.staticflickr.com/2500/3690358997_7474c2eac5.jpg">CC2.0</a><br />
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*The species name means, I guess, "looks like a&nbsp;<a href="http://en.wikipedia.org/wiki/Crane_fly">crane fly</a>"... don't see it myself</div>
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David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com5tag:blogger.com,1999:blog-4718577088343779246.post-24525353194878221682012-12-02T18:46:00.003+13:002012-12-02T19:20:54.292+13:00Sunday Spinelessness - Bark LiceI should have known that the <a href="http://sciblogs.co.nz/the-atavism/2012/11/25/sunday-spinelessness-an-id-challenge/">little challenge I put up last week</a>&nbsp;wouldn't so much as wrinkle the brow of the bug-blogo-sphere's best. <i>The Atavism</i>'s two homes means there were two winners. Ted MacRae of <i><a href="http://beetlesinthebush.wordpress.com/author/tcmacrae/">Beetles in the Bush</a>&nbsp;</i>chimed in at he blogspot version,&nbsp;correctly identifying the insect as a "bark louse" or p<a href="http://en.wikipedia.org/wiki/Psocoptera">socopteran</a>, and recognizing those stubby white&nbsp;protrusion&nbsp;as yet-to-be expanded wings .&nbsp;Morgan Jackson of <i><a href="http://www.biodiversityinfocus.com/blog/">Biodiversity in Focus</a></i>&nbsp;did the same at SciBlogs.<br />
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Thanks too to Deborah from <a href="http://beefaerie.wordpress.com/"><i>Bee of a Certain Age</i></a>, who hazarded a guess that those white protrusions might be eggs. Certainly a more reasonable guess that my own first thoughts at seeing these bugs crawling over the the Big Tree* in our garden. The plump&nbsp;abdomens and long antennae made me think of the large (but certainly not <a href="http://sciblogs.co.nz/the-atavism/2010/08/29/sunday-spinelessness-new-zealands-giant-sprintgtails/">GIANT</a>)&nbsp;<a href="http://en.wikipedia.org/wiki/Entomobryomorpha">springtails</a>. Ripping up a couple of pieces of bark&nbsp;revealed&nbsp;a whole colony of these odd-looking bugs, and evidence for just how wrong I was.&nbsp;</div>
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The adults have wings, which they hold tent-like over their bodies. Insects are the only invertebrates with wings, so, since&nbsp;spring tails&nbsp;aren't insects, my first guess was horribly inaccurate (glossing over about 400 million years of&nbsp;evolutionary&nbsp;divergence).<br />
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As Ted and Morgan worked out, these are "bark lice", members of the order Psocoptera. Although they are related to the "true lice" (Order&nbsp;Phthiraptera), psocopterans are not parasites. Rather, they wander around their trees eating algae, fungi and whatever&nbsp;detritus might be clinging to the bark. The only species that could be considered pests are the "<a href="http://psocopterans/">book lice</a>" - small flightless&nbsp;psocopterans&nbsp;that&nbsp;sometimes&nbsp;turn up in old books where they eat the paste that binds pages together. (<a href="https://twitter.com/theobrominated/status/275118177619427328">I have it on good authority</a>&nbsp;that book lice can also destroy botanical collections, so certainly a pest)<br />
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A couple of weeks ago I gave Veronika Meduna a tour of our garden and its bugs, and I gather you can hear the&nbsp;result&nbsp;on Radio New Zealand's <i><a href="http://www.radionz.co.nz/national/programmes/ourchangingworld">Our Changing World</a> </i>next week. While I was catching my breath between talking about the mating habits of spiders, and how <a href="http://nzetc.victoria.ac.nz/tm/scholarly/tei-Bio25Tuat02-t1-body-d2.html">our native slugs are much more sluggish then their introduced counterparts</a>&nbsp;she asked the obvious question - "why?". Why do I care so much about odd little creatures like bark lice and slugs and spiders? I'm not sure I managed a&nbsp;coherent&nbsp;answer at the time, but I can tell you now, spineless creatures need&nbsp;evangelists because most people have a very skewed view about the way biology works.&nbsp;If your vision of biodiversity is limited to pandas and dolphins and lions and tigers then you are missing out on millions of other ways to be alive.<br />
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Take bark lice as an example. I'll admit that I'd never given these creatures a moments thought &nbsp;before running into them last week. But, in researching this post I found out there are more than four thousand psocopteran species. That is to say, there are almost as many bark lice species as there are mammals - all the lions, tigers, bears, dolphins, whales, marsupials, rodents and bats in the world add up to about 5 400. That matters because species are the fundamental units of biological diversity. Each species represents a distinct evolutionary lineage - free to take up different ecological niches, develop new&nbsp;morphological&nbsp;features or occupy a different geographic range.<br />
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To try an illustrate how diverse these unassuming little critters really are, I've put together a "<a href="http://en.wikipedia.org/wiki/Treemapping">treemap</a>". In the plot below, each of the stained-glass window panels represents the number of species in one&nbsp;psocopteran genus, nested within a family (the heavier lines, with labels ending in -DAE) which in turn is nested within a suborder (the very heaviest lines, labeled -MORPHA). These higher taxonomic ranks are not fundamental units in the way species are. Even so, species placed within a&nbsp;taxonomic&nbsp;group share evolutionary history, and are united by particular morphological characters which they share. &nbsp;It turns out there are quite a few ways to be a bark louse:<br />
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And that's just bark lice!<br />
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For me, this chart is the best answer to "why?". How can you know you share the world with all this&nbsp;extraordinary&nbsp;diversity and not want to want to spend your time working out how it got here?</div>
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*This is not a botany blog... I really have no idea what the tree is</div>
David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-67023707404823639542012-11-25T20:09:00.002+13:002012-11-25T21:34:35.217+13:00Sunday Spinelessness - An ID challenge <div style="text-align: center;">
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OK, here's a chance for the bug nerds to show off. A photo of a strange-looking beast I recently ran into:</div>
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The challenge to readers is to answer the two questions that went through my head when I first uncovered the creature (1) What the hell is that? (2) What's going with those opaque white projections?</div>
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<a href="http://myrmecos.net/category/mysteries/">Unlike others</a>, I can't often you anything cool as a prize for being right, but surely an electronic record to your entomological know-how will be enough?</div>
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David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com2tag:blogger.com,1999:blog-4718577088343779246.post-61272837977742923022012-11-18T15:45:00.000+13:002012-11-18T15:45:26.185+13:00Sunday Spinelessness - Shocked from sloth by a beautiful spiderRegular readers will know that I've been pretty slack in posting here in recent weeks. Just the same old boring reason - lots of "real" work to get done and, as much as I enjoy it, blogging necessarily floats to the bottom of TODO lists.<br />
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But I was shocked from my sloth&nbsp;this afternoon&nbsp;when I passed that <a href="http://sciblogs.co.nz/the-atavism/2010/07/25/sunday-spinelessness-a-missed-opportunity/">accursed agapanthus</a>&nbsp;and saw a spider I really had to share with the world:<br />
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It's an orb-weaving (<a href="http://en.wikipedia.org/wiki/Orb-weaver_spider">araneid</a>) spider, a relative of the familiar garden spiders like the very common&nbsp;<i>Eriophora pustulosa </i>that spin orb-shaped webs and catch unlucky flying insects. I can't be sure on the identification of this one, but I reckon (with some support from twitter's&nbsp;resided&nbsp;spider experts, [<a href="https://twitter.com/nsandlin">1</a>], [<a href="https://twitter.com/sc_evans">2</a>]) its a species a species of&nbsp;<i>Novaranea.&nbsp;</i>According to <a href="http://www.teara.govt.nz/en/spiders-and-other-arachnids/1/5">Ray and Lyn Foster's</a> &nbsp;<a href="http://www.otago.ac.nz/press/booksauthors/2005/forster.html">Big Spider Book</a>&nbsp;New Zealand&nbsp;<i>Novaranea</i>&nbsp;species are most commonly encountered in in grasslands and tussocks, so&nbsp;perhaps&nbsp;this one blew in from the tall grass that covers some the abandoned&nbsp;gardens in our block.<br />
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However it made it our garden, I'm very happy to have encountered a such a neat looking spider, and even done a half-decent job capturing some of its beauty:
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David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-86206898443099763932012-09-25T20:07:00.001+12:002012-09-25T20:07:44.144+12:00All the media!Oh, hi there. Yeah, it's been a while h'uh? Just been crazy busy lately you know - one thing after another with manuscripts and datasets to analyse, then I got a whole bunch of lab reports to mark. We should totally like, get back to writing/reading about science though. I'll put something up in a bit and...*<br />
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So, things have been a little quite here lately. That wasn't a plan to have me an<a href="http://sciblogs.co.nz/the-atavism/2012/08/28/graduation-nerd-blogging-and-a-talk/"> that&nbsp;ridiculous&nbsp;hat </a>up on the front page for a few weeks - just the result of having little spare time. As it turns out, a few things that might be of interest to readers here have been published over that fallow period, here's the links:<br />
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<li>I'm in a book! As I related last year, my post on the partulids land snails of Society Isalnds was selected for <i><a href="http://books.scientificamerican.com/fsg/books/the-best-science-writing-online-2012/">The Best Science Writing Online</a>&nbsp;</i>which is now&nbsp;available&nbsp;from all good book sellers. I'm&nbsp;ridiculously&nbsp;excited by this. There is also a short review in <a href="http://www.listener.co.nz/current-affairs/science/the-genomic-zoo/"><i>The Listener</i>&nbsp;</a></li>
<li><a href="http://www.stuff.co.nz/science/7645232/Science-misapplied-in-gay-debate">My latest little piece for stuff.co.nz</a> deals with Colin Craig and his idea that research tells us sexual orientation is a choice, and that this is relevant to marriage equality.&nbsp;</li>
<li><a href="http://www.mixcloud.com/Radio_One_91fm_Dunedin/rush-hour-5912-with-gerard-barbalich/">I was on the radio</a> - an hour of talking about science, peer review and skepticsm on Radio One, the student radio station.</li>
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I guess to complete the set I'd need to make a TV&nbsp;appearance, though I can't see that happening!<br />
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*For people with whom I've had exactly this conversation lately - it's true, I have been busy, I am a terribly friend and we <i>will</i> catch up soon!David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com3tag:blogger.com,1999:blog-4718577088343779246.post-6217832394471194052012-08-28T11:35:00.001+12:002012-08-28T11:39:39.295+12:00Graduation, nerd blogging and a talkThe most dedicated readers of <i>The Atavism</i> may have noticed a few Sundays have passed without&nbsp;celebration&nbsp;of a spineless creature. <a href="http://itsbeenawhilesincemylastpost.blogspot.co.nz/">Well, you know how blogging is sometimes</a>. A few of the things that have kept me from blogging might be of interest to readers here. This weekend was dedicated to the wearing of silly hats, posing somewhat awkwardly and the conferring of my PhD. It was almost a big enough event to make me wear a tie:<br />
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So far I've&nbsp;rested&nbsp;the urge to change the name that appears under these posts to Dr David Winter, we'll see how long that lasts.<br />
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I've also been working a little on some more software for&nbsp;evolutionary&nbsp;biology. Since I very much aim this blog at a lay-level, and there is no reason on earth why a lay-person ought to care about the computer programs scientists use to collect and analyse their data, I've decided to set up a <a href="http://dwinter.github.com/">dedicated nerd blog</a>. The first post their introduces <a href="http://dwinter.github.com/blog/2012/08/14/rentrez-an-r-package-for-interfacing-with-the-ncbis-databases/">an R library that can help researchers quickly download data from molecular biology and medical databases</a>.<br />
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Finally, I should say their probably won't be a new post here this weekend either, as I'll be at the New <a href="http://www.skeptics.org.nz/SK:SKEPCONFERENCE:1133748200">Zealand Skeptics Conference</a>, right here in Dunedin. I'll be giving a talk about how the the creation-evolution "debate" as it usually plays out has very little to do with&nbsp;evolutionary&nbsp;biology, and how getting past popular misconceptions about the way evolution works makes most creationist objections to evolution into non-starters. I'll also say why I think good old fashioned creationism is a more respectable position than "intelligent&nbsp;design", so that ought to be fun. If you're in Dunedin you can still register for&nbsp;the&nbsp;whole meeting, my talk is on at 9:50am on&nbsp;Saturday&nbsp;in Archway 3 (the best, and&nbsp;perhaps&nbsp;only, way to find this lecture theatre is to walk into the Archway building and wander around opening doors at random).David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-62384350659132898392012-08-09T11:00:00.000+12:002012-08-09T11:00:43.294+12:00Measuring population differentiation in R<span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org/"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border: 0;" /></a></span>
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<span style="background-color: white;">This is a little bit different than most posts here. I have a paper out today in </span><i style="background-color: white;">Molecular Ecology Resources</i><span style="background-color: white;">:</span><span style="background-color: white;">&nbsp; "mmod: an R library for the calculation of population differentiation statistics" (doi: <a href="http://dx.doi.org/10.1111/j.1755-0998.2012.03174.x">10.1111/j.1755-0998.2012.03174.x</a>). Looking around the web, there aren't many simple expositions of just what a "differentiation statistic" might be, and why the "modern measures of differentiation" my little R package can calculate might improve on the more traditional ones. So, &nbsp;</span><span style="background-color: white;">I thought I'd have a go here.&nbsp;</span><br />
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Biologists often want to be able to measure the degree to which a&nbsp;population&nbsp;is divided into smaller&nbsp;sub-populations. This can be an important thing to&nbsp;quantify, because sub-populations within highly&nbsp;structured populations are, to some extent, genetically distinct from other&nbsp;sub-populations&nbsp;and therefore have their own evolutionary histories (and perhaps futures).<br />
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To illustrate this point I've run some simulations. Imagine if we had 5 subpopulations, each with a thousand individuals. In each population we will follow the fate of a locus with two alleles, <i>R</i> and <i>r</i>&nbsp;that have no effect on survival or reproduction and start with frequencies 0.8 and 0.2 respectively (<a href="http://sciblogs.co.nz/the-atavism/2012/07/11/you-cant-ban-redheaded-sperm/">these numbers motivated by this post)</a><span style="background-color: white;">. In the absence of gene flow between these populations (Panel 1) the frequency of the <i>r</i>&nbsp;allele&nbsp;bounces&nbsp;around due to genetetic drift (evolutionary change, after all, is inevitable). Crucially though, changes in one population can't effect other populations so we end up with substantial among-population differences in allele frequency. In the next two panels,&nbsp;</span><span style="background-color: white;">in each generation</span><span style="background-color: white;">&nbsp;a proportion of each population's individuals (0.001 and 0.01 respectively)&nbsp;</span><span style="background-color: white;">are drawn from the other populations in the simulation.&nbsp;</span><span style="background-color: white;">Now that the populations are sharing genes the lines that represent their allele frequencies pull together &nbsp;(that is, the among-population variation is reduced).&nbsp;</span><br />
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<span style="background-color: white;">One way to&nbsp;quantify&nbsp;the among-population variation displayed in these simulations is to look at the number of heterozygotes you expect to observe across the entire population. The final values for P(</span><i style="background-color: white;">r</i><span style="background-color: white;">) in the first simulation were {0.33, 0.47. 0.88. 0.10. 0.33} with a mean frequency of 0.42 (so the frequency of the </span><i style="background-color: white;">R </i><span style="background-color: white;">allele would be&nbsp;0.58). Knowing our </span><a href="http://sciblogs.co.nz/the-atavism/2012/07/11/you-cant-ban-redheaded-sperm/" style="background-color: white;">Hardy Weinberg</a><span style="background-color: white;">, if we had one big population with two alleles, one being at a frequency of 0.42 we'd expect to get </span><b style="background-color: white;">2pq = 2 * 0.42 * 0.58 = 0.40 </b><span style="background-color: white;">heterozygotes. We can call that number </span><i style="background-color: white;">H<sub>T&nbsp;</sub></i><span style="background-color: white;">for&nbsp;</span><span style="background-color: white;">expected&nbsp;</span><span style="background-color: white;">total heterozygosity. But thats not what we'd actually see in this case. The&nbsp;sub-populations&nbsp;that make up this larger&nbsp;population&nbsp;have their own allele frequencies, when we calculate the expected proportion of heterozygotes for each of these populations by themselves we end up with </span><span style="background-color: white;">{0.44, 0.49, 0.21, 0.18, 0.44} for a within-population expected heterozygosity (</span><i style="background-color: white;">H<sub>S</sub></i><span style="background-color: white;">) of 0.35*. This lack of heterozygotes within sub-populations compared with the total population expectation will always arise when genetic drift&nbsp;makes&nbsp;sub-populations distinct from each other.&nbsp;
<a href="http://en.wikipedia.org/wiki/Masatoshi_Nei">Masatoshi Nei&nbsp;</a>&nbsp;used this pattern to propose a statistic to quantify&nbsp;population divergence called <i>G</i></span><i style="background-color: white;"><sub>ST,&nbsp;</sub></i><span style="background-color: white;">which he defined</span><span style="background-color: white;">&nbsp;</span><span style="background-color: white;">like this:</span><br />
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<i>&nbsp;G<sub>ST = </sub></i><span style="background-color: white;">(</span><i style="background-color: white;">H<sub>T </sub></i><i style="background-color: white;">-&nbsp;</i><span style="background-color: white;"><i>H</i><sub><i>S</i> </sub></span><span style="background-color: white;">)&nbsp;</span><i style="background-color: white;">/&nbsp;</i><i style="background-color: white;">H<sub>T</sub></i></div>
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<span style="background-color: white;">Nei's motivaton with&nbsp;</span><span style="background-color: white;">G</span><i style="background-color: white;"><sub>ST&nbsp;</sub></i><span style="background-color: white;">was to generalise <a href="http://en.wikipedia.org/wiki/Sewall_Wright">Sewall Wright</a>'s <i>F</i></span><i style="background-color: white;"><sub>ST </sub></i><span style="background-color: white;">**, which was defined for diploid organisms and two-allele systems, so that it could be used for any genetic data. But there's a problem with this formulation. Because&nbsp;</span><span style="background-color: white; text-align: center;"><i>H</i><sub><i>T </i>&nbsp;</sub></span><span style="background-color: white;">is always larger than&nbsp;</span><i style="background-color: white; text-align: center;">H<sub>S&nbsp;</sub></i><span style="background-color: white;">&nbsp;and can't be greater than one, the maximum possible value of&nbsp;</span>
<i style="text-align: center;">G<sub>ST&nbsp;</sub></i>&nbsp;<span style="background-color: white;">is 1-</span><i style="background-color: white; text-align: center;">H<sub>S</sub></i><span style="background-color: white;">. This dependency on the within-population genetic diversity means comparisons between studies, and even between loci in one study, are difficult (since&nbsp;</span><i style="background-color: white; text-align: center;">H<sub>S&nbsp;</sub></i><span style="background-color: white;">will likely be different in each case). This is&nbsp;particularly&nbsp;worryingly for highly polymorphic makers like</span><span style="background-color: white;">&nbsp;<a href="http://en.wikipedia.org/wiki/Microsatellite">microsatellites</a>, which can give values of&nbsp;</span><i style="background-color: white; text-align: center;">H<sub>S</sub></i><span style="background-color: white;">&nbsp;as high as 0.9, severely constraining the possible values of&nbsp;</span><i style="background-color: white; text-align: center;">G<sub>ST</sub></i><span style="background-color: white;">.</span><br />
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<span style="background-color: white;">Although the problem of&nbsp;</span>
<i style="text-align: center;">G<sub>ST</sub></i><span style="background-color: white;">'s dependence on&nbsp;</span><i style="background-color: white; text-align: center;">H<sub>S</sub></i><span style="background-color: white;">&nbsp;has been known for a while, it's taken some time for new statistics that get around this problem to be developed. Philip Hedrick&nbsp;</span><span style="background-color: white;">(doi:&nbsp;</span><a href="http://dx.doi.org/10.1016/10.1554/05-076.1" style="background-color: white;">10.1554/05-076.1</a><span style="background-color: white;">) along with</span><span style="background-color: white;">&nbsp;Patrick&nbsp;</span><span style="background-color: white;">Meirmans (doi:&nbsp;<a href="http://dx.doi.org/10.1111/j.1755-0998.2010.02927.x">10.1111/j.1755-0998.2010.02927.x</a>) introduced&nbsp;</span><i style="background-color: white; text-align: center;">G''<sub>ST</sub></i><span style="background-color: white;">&nbsp;</span><span style="background-color: white;">&nbsp;- a version of&nbsp;</span><i style="background-color: white; text-align: center;">G<sub>ST&nbsp;</sub></i><span style="background-color: white;">that is corrected for the observed value of&nbsp;<i style="background-color: white; text-align: center;">H<sub>S</sub></i>&nbsp;as well as the number of sub-populations being considered.&nbsp;</span><span style="background-color: white;">Meirmans</span><span style="background-color: white;">&nbsp;used a similar trick to define </span><span style="background-color: white; font-family: sans-serif; font-size: 13px; line-height: 19px; text-align: -webkit-auto;">φ'</span><i style="background-color: white; text-align: center;"><sub>ST &nbsp;</sub></i><span style="background-color: white;">(doi:&nbsp;<a href="http://dx.doi.org/10.1111/j.0014-3820.2006.tb01874.x">10.1111/j.0014-3820.2006.tb01874.x</a>), another&nbsp;</span><span style="background-color: white;"><i>F</i></span><i style="background-color: white;"><sub>ST&nbsp;</sub></i><span style="background-color: white;">analogue that partitions genetic distances into within- and between-population components. Most recently, Lou Joust introduced an entirely&nbsp;separate&nbsp;statistic, <i>D</i>, that &nbsp;directly measures&nbsp;allelic&nbsp;divergence (doi <a href="http://dx.doi.org/10.1111/j.1365-294X.2008.03887.x">10.1111/j.1365-294X.2008.03887.x</a>).&nbsp;</span><br />
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<span style="background-color: white;">The <a href="http://www.r-project.org/">statistical programming language R</a> is becoming increasingly popular among biologists. Although there is a strong suite of tools for performing population genetic analyses in R, code to calculate these "new" measures of population divergence have not been&nbsp;available. My package, mmod, fills this gap. &nbsp;I won't give too many details of the package here, as that's detailed in the paper and the package is will documented. Briefly, mmod has functions to calculate the three statistics described above (and Nei's&nbsp;</span>
<i style="text-align: center;">G<sub>ST</sub></i>&nbsp;<span style="background-color: white;">), as well as pairwise versions of each statistic for every&nbsp;population&nbsp;in a&nbsp;datastet. It also allows users to perform bootstrap and jacknife&nbsp;re-sampling&nbsp;of datasets, the results of which are returned as user-accessable objects which can be examined with any R function (there is also a helper function to easily apply differentiation statistics to bootstrap sample and summarise the results) . The library is on CRAN, so installation is as easy as typing "install.pacakge("mmod")", the <a href="https://github.com/dwinter/mmod/">source code is up on github</a>. If want to use the package I'd suggest reading the vignette ("mmod-demo") before you dive in.</span><br />
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<span style="background-color: white;"><span style="background-color: white;">I'm keen to hear about bugs or feature requests from users, just email them to david.winter@gmail.com</span></span><br />
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<span style="background-color: white;"><b>Reference</b>:</span><br />
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<span style="background-color: white;">Winter, D.J. (in press). MMOD: an R library for the calculation of population differentiation statistics<span style="font-style: italic;">Molecular Ecology Resources</span>&nbsp;:&nbsp;<a href="http://dx.doi.org/10.1111/j.1755-0998.2012.03174.x" rev="review">dx.doi.org/10.1111/j.1755-0998.2012.03174.x</a></span><br />
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<span style="background-color: white;">* mmod actually uses nearly unbiased estimators for these parameters, to deal with the way small population samples can mis-represent the actual allele frequencies in populations.</span></div>
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<span style="background-color: white;">** I don't want to write an entire history of F-statisitcs here, because it's a big and murky topic, but I did want to make the point that the formulation I gave for <i>G</i><i style="background-color: white;"><sub>ST &nbsp;</sub></i><span style="background-color: transparent; text-align: -webkit-auto;">is often presented as "Wright's&nbsp;</span></span><span style="background-color: white;"><i>F</i></span><i style="background-color: white;"><sub>ST </sub></i><span style="background-color: white;"><span style="background-color: transparent; text-align: -webkit-auto;">" in genetics courses. Wright was certainly aware that his statistic was related to the proportion of heterozygotes you expect to get in a populaiton, but,</span></span><span style="background-color: white;"><span style="background-color: transparent; text-align: -webkit-auto;">&nbsp;when he introduced F-statistics in general, and&nbsp;</span></span><span style="background-color: white;"><i>F</i></span><i style="background-color: white;"><sub>ST &nbsp;</sub></i><span style="text-align: -webkit-auto;">in particular, he was really dealing with correlation among gametes at various levels of population structure. Unfortunately, there are now many many definitions of&nbsp;</span><span style="background-color: white;"><i>F</i></span><i style="background-color: white;"><sub>ST &nbsp;</sub></i><span style="text-align: -webkit-auto;">floating around, and it's probably pointless to argue about a "right one". If you use my package I encourage you to be explicit about, and cite, the particular statistic that you are using. For each of the the&nbsp;</span><span style="background-color: white;"><i>F</i></span><i style="background-color: white;"><sub>ST&nbsp;</sub></i>&nbsp;analogues that&nbsp;the package calculates the in-line help contains the correct&nbsp;reference.&nbsp;</div>
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</div>David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-73430767851074417682012-08-05T14:12:00.000+12:002012-08-06T10:02:29.318+12:00Sunday Spinelessness - How snails conquered the land (again and again)<div class="separator" style="clear: both; text-align: center;">
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Christie Willcox wrote a <a href="http://blogs.scientificamerican.com/science-sushi/2012/07/28/evolution-out-of-the-sea/">nice article this week</a> on how one small group of organisms called "vertebrates" first evolved to live on land. Since you are a vertebrate who lives on land, you should probably go and read Christie's piece. I wouldn't want you, however, to go around thinking those first fish to leave the ocean behind were pioneers making a uniquely difficult transition. By my figuring, onycophorans (velvet worms like <a href="http://sciblogs.co.nz/the-atavism/2010/08/15/sunday-spinelessness-peripatus/">peripatus</a>), tardigrades, annelids, nematodes, nemerteans (<a href="http://en.wikipedia.org/wiki/Nemertea">ribbon worms</a>) and quite a few arthropod lineages have also taken up a terrestrial lifestyle. Many of those lineages were already breathing air before <i>Tiktaalik,</i>&nbsp;<i>Ichthyostega </i>and your other long-lost relatives<i>&nbsp;</i>came along to join them on land. But if you want to talk about transitions from marine to terrestrial lifestyles then you really want to talk about snails. You can find snails living in &nbsp;almost every habitat between the deep ocean and the desert, and snails have adapted to life on land many different times. In fact, a litre of leaf litter taken from a New Zealand forest can contain snails representing three&nbsp;separate&nbsp;transitions from water to land.<br />
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Almost all the land snails I've talked about here at <i>The Atavism</i>&nbsp;are descendants from just one invasion of the land. We call these species the&nbsp;<a href="http://en.wikipedia.org/wiki/Stylommatophora">stylommatophorans</a>&nbsp;and you can tell them from other landlubber-snails because they&nbsp;have eyes on stalks (as modeled here by&nbsp;&nbsp;<i>Thalassohelix igniflua</i>):<br />
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These snails are part of a larger group of air-breathing slugs and snails (including species living in fresh water, &nbsp;estuaries and even the ocean) called pulmonates or "lung snails". As both the common and the scientific names suggest, pulmonates breathe with lungs. Specifically, the mantle cavity, which contains gills in sea snails, is perfused with fine veins that allow oxygen to permeate the snails's blood. In&nbsp;relatively&nbsp;thin-shelled species you can often see this "vasculated" tissue in living animals:</div>
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Blacklight photo of <i>Cepaea nemoralis</i> showing 'vascularised' lung. Photo is <a href="http://creativecommons.org/licenses/by-sa/3.0/deed.en">CC BY-SA </a>via&nbsp;Wikipedian <a href="http://en.wikipedia.org/wiki/User:Every1blowz">Every1Blowz</a></div>
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The pulmonates can also regulate the amount of air entering their lungs with the help of an organ called the pneumatostome or breathing pore - &nbsp;an opening to the mantle cavity that the snail can open or close at will:<br />
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<span style="font-size: 85%;">A leaf-veined slug from my garden - the small opening near the "centre line" of the slug is the pneumatostome. Interestingly, leaf-veined slugs don't have lungs, the pneumatostome opens to a series of blind tubes not unlike an insect's&nbsp;respiratory system</span></div>
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So that, along with a whole load of adaptations that prevent a fundamentally wet animal from drying out, is your basic land snail. But those <a href="http://sciblogs.co.nz/the-atavism/tag/native-snails/">little leaf-litter snails I've been talking about for the last couple of weeks</a> provide a good reminder that other snail lineages have left the life aquatic. Here's a species you find almost everywhere there is native forest in Otago, <i>Cytora tuarua</i>:<br />
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Holotype of <i>Cytora tuarua</i> B. Marshall and Barker, 2007. Photo is from Te Papa Collectons onlne, and provided under a <a href="http://creativecommons.org/licenses/by-nc-nd/3.0/nz/deed.en">CC BY-NC-ND license</a></div>
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<i>Cytora</i> is from the superfamily Cyclophoroidea, a group of snaisl that have indepedantly adapted to life on (relatively) dry land. (<a href="http://sciblogs.co.nz/the-atavism/2012/07/29/sunday-spinelessness-hairy-snails/">The weirdly un-twisted <i>Opisthostoma </i>is in this post </a>is another cyclophoroid). &nbsp;Cyclophoroids share some&nbsp;stylommatophoran adaptations to life on land, they've lost their gills and replaced them with a heavily&nbsp;vesculalised mantle cavity. Slightly oddly, cyclophoroids also breathe with their kidneys. Or, at least, the nephridium, an organ which does the same job as a vertebrate kidney, includes "vascular spaces" that the snail can use to collect oxygen from the air. Cyclophoroids don't have an organ equivalent to the&nbsp;breathing&nbsp;pore to control the flow of air into the mantle cavity. Instead the mantle cavity is open and air enters by&nbsp;diffusion, or in larger species, as the result of movements of the animals head.&nbsp;</div>
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For the most part, the&nbsp;respiratory and&nbsp;excretory&nbsp;systems in&nbsp;cyclophoroids are not as well adapted to life on land as those in their&nbsp;stylommatophoran cousins. For this reason, most&nbsp;cyclophoroids are only active in very humid conditions.&nbsp;In my limited experience, <i>Cytora</i>&nbsp;species are usually found deep in moist leaf litter and soil samples, and I've never seen one crawling about. Nevertheless, some species can survive in drier situations, and these are certainly terrestrial snails.</div>
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Local leaf litter samples reveal a third move from the water to land. I don't have nice photo of <i>Georissa purchasi, </i>and I can't find anything else on the web either, so you're stuck with a crumby drawing from my notebook:<br />
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<img src="http://i.imgur.com/rWjLY.jpg" width="400px" /><br />
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I did warn you that it was a crumby drawing. In life&nbsp;<i>G. purchasi </i>have an orange-red sort of a hue, and you can often see patches of pigment from the animal through the shell. &nbsp;<i>Georissa</i>&nbsp;species are from the family Hydrocenidae and are quite closely related to a group of predominantly freshwater snails called <a href="http://en.wikipedia.org/wiki/Neritidae">nerites</a>. Just like the other lineages discussed, the&nbsp;Hydrocenidae have given up their gills and breathe through a vasculated mantle cavity. Very little is known about the biology of these snails.&nbsp;<i>G. purchasi </i>is sometimes said to be limited to very wet conditions, but I've collected (inactive) specimens form the back of fern fronds well above ground so it can't be completely&nbsp;allergic&nbsp;to dry .&nbsp;</div>
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So, in a handful of leaf litter collected from a Dunedin park you might have cyclophoroids, hydrocenids and &nbsp;stylommatophorans - descendants from three different moves from sea to land. If we look a little more broadly, &nbsp;there are are many more examples of this transition. &nbsp;I've written about the&nbsp;<a href="http://sciblogs.co.nz/the-atavism/2009/12/13/sunday-spinelessness-a-snail/">the helicinids</a> before, then there are&nbsp;terrestrial&nbsp;littorines (perwinkle relatives) some of which have both gills and lungs. Plenty of other pulmonate lineages that have also taken up an entirely terrestrial lifestyle. Because some of these groups have adapted to life on land multiple times, there have probably been more than 10 invasions of the land by snails.</div>
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Most of the description of Cyclophoroids here is taken from:<br />
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Barker, GM (2001)&nbsp;Gastropods on land: phylogeny, diversity and adaptive morphology In Barker (Ed.), &nbsp;<i><a href="http://bookshop.cabi.org/default.aspx?site=191&amp;page=2633&amp;pid=281">The biology of terrestrial molluscs</a>&nbsp;(</i>pp 1<span style="background-color: white; font-family: sans-serif; font-size: 13px; line-height: 19px;">—</span>146)<i>&nbsp;</i>CABI Publishing.David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-14449091996443562502012-07-29T20:08:00.000+12:002012-07-29T20:08:25.352+12:00Sunday Spinelessness - Hairy snails<div style="text-align: left;">
Here's another of these <a href="http://sciblogs.co.nz/the-atavism/2012/07/22/sunday-spinelessness-new-zealand-microsnails/">tiny native snails I talked about last week</a>. <i>Aeschrodomus stipulatus</i>:<br />
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Not the best photo I'll admit, but it records enough detail to see the two things that set&nbsp;<i>Aeschrodomus</i>&nbsp;apart from most of its relatives in New Zealand. It's tall and hairy. I'm not sure if there is an accepted definition of "hair" when it comes to snail shells, but plenty of different land snails groups have developed processes that extend form the shell. In New Zealand we have the fine bristles of <i><a href="http://www.teara.govt.nz/en/native-plants-and-animals-overview/2/5">Suteria ide</a>, </i>the filaments of&nbsp;<i>Aeschrodomus</i>&nbsp;and the spoon-shaped processes of <i>Kokopapa</i>&nbsp;(literally&nbsp;"spoon-shell"):</div>
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<i>K. unispathulata</i> <a href="http://blog.doc.govt.nz/2012/06/29/volunteer-spotlight-david-roscoe/">Photo is from David Roscoe / DoC</a>&nbsp;and is under Crown Copyright<br />
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I try very hard to avoid the sloppy thinking that presumes there is an adaptive&nbsp;explanation&nbsp;for every biological observaton, but it's hard to see how these hair-like processes would evolve if they didn't serve a purpose. The larger hairs are presumably made from the same calcium carbonate minerals as the rest of shell, and calcium is a&nbsp;precious&nbsp;resource for snails (so much so that empty shells collected from the field often show signs of having been partially eaten by living snails). In those species with finer projections, the hairs are an extension of the "periostracum", a protein layer that covers snail shells. &nbsp;If we presume that snail hairs come at a cost, in either protein or calcium, what reward are they hairy snails reaping from their investment?</div>
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<a href="http://user.uni-frankfurt.de/~markusp/">Markus Pfenninger</a> and his colleagues asked just that question by looking at snails from the Northern&nbsp;Hemisphere&nbsp;genus&nbsp;<i>Trochulus </i>(<span style="background-color: white;">doi:&nbsp;</span><a href="http://www.blogger.com/dx.doi.org/10.1186/1471-2148-5-59" style="background-color: white;">10.1186/1471-2148-5-59</a><span style="background-color: white;">).&nbsp;</span><span style="background-color: white;">This genus contains many species that sport very fine and soft hairs.&nbsp;</span><span style="background-color: white;">Pfenninger</span><span style="background-color: white;">&nbsp;</span><i>et al.</i>collected ecological data for each species, and used DNA sequences to estimate a the evolutionary relationships between those species. From these data, they were able to infer the common ancestor of modern&nbsp;<i>Trochulus</i> species was probably hairy, and three&nbsp;separate&nbsp;losses of hairyness can explain all the among-species variation in this trait. Moreover, it appears the loss of hairs in&nbsp;<i>Trochulus</i><span style="background-color: white;">&nbsp;is</span><span style="background-color: white;">&nbsp;associated&nbsp;with a switch for wet to dry habitats. Given this finding, Pfenninger's team hypothesised that, in&nbsp;</span><i>Trochulus</i>&nbsp;at least, hirsute snails might stick to host plants more effectively than their bald brethren. Indeed, in experiments it took more force to dislodge a hairy shell from a wet leaf than non-hairy one.<br />
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Pfenninger's study makes a neat case for the&nbsp;maintenance&nbsp;of hairy shells in Trochulus, but I don't think adherence to leaves can explain all the hairy snails we know about. In New Zealand, most snails with shell processes are limited to leaf litter, a habitat that would seem to make adhering to leaves a positive&nbsp;hindrance&nbsp;to getting around. I don't know if we'll ever have a simple answer as to why some of our snails sport these attachments, but&nbsp;<a href="http://science.naturalis.nl/schilthuizen">Menno Schilthuizen</a>'s work might give us a couple of clues as to why these sorts of shell&nbsp;sculpture&nbsp;arise and stick around. In 2003,&nbsp;Schilthuizen proposed many shell features may arise because those individuals that have them are more likely to procure a mate (or perhaps a&nbsp;desirable&nbsp;mate) (doi: <a href="http://dx.doi.org/10.1186/1471-2148-3-13">10.1186/1471-2148-3-13</a>). Although there is quite a lot of evidence for sexual selection in land snails, I don't know of a study testing&nbsp;<span style="background-color: white;">Schilthuizen's hypothesis on shell&nbsp;sculpture. On the other hand,&nbsp;</span><span style="background-color: white;">Schilthuizen's group has found evidence that elebaroate shell sculpture can arise as a response to predation (doi:&nbsp;</span><span style="background-color: white;"><a href="http://dx.doi.org/10.1111/j.0014-3820.2006.tb00528.x">10.1111/j.0014-3820.2006.tb00528.x</a>).&nbsp;</span><span style="background-color: white;"><i>Opisthostoma </i>land snails from Borneo have extradonary shells, with unwound shapes, ribs and spines:</span></div>
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<img src="http://upload.wikimedia.org/wikipedia/commons/7/76/Opisthostoma_mirabile_shell.png" /></div>
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<i>Opisthostoma mirabile</i></div>
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In Borneo,&nbsp;<i style="background-color: white; text-align: center;">Opisthostoma </i><span style="background-color: white; text-align: center;">species&nbsp;</span><span style="background-color: white; text-align: center;">live alongside a predatory slug that attacks these snails by boring a hole into their shells. The unique shape and ornamentation of&nbsp;</span><i style="background-color: white; text-align: center;">Opisthostoma</i><span style="background-color: white; text-align: center;">&nbsp;shells appears to have evolved to hinder slug attacks. Even more interestingly, geographically distinct populations of slug appear to attack snails in different ways. This local variation in predator&nbsp;behavior&nbsp;could well be a response to local variation in the shell ornamentation - a so called <a href="http://en.wikipedia.org/wiki/Red_Queen%27s_Hypothesis">Red Queen</a> process in which each population evolves&nbsp;rapidly while maintaining more or less the same <a href="http://en.wikipedia.org/wiki/Fitness_(biology)#Relative_fitness">relative fitness</a>.&nbsp;</span></div>
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<span style="background-color: white; text-align: center;">There are certainly plenty of snail-eating animals in New Zealand. Several&nbsp;species&nbsp;of&nbsp;<i>Wainuia </i>land snail appear to&nbsp;specialise&nbsp;in eating micro snails, which they scoop up and carry off using a "prehensile&nbsp;tail" (Efford, 1998 [<a href="http://www.doc.govt.nz/upload/documents/science-and-technical/sfc101.pdf">pdf</a>]). It's entirely possible that the relatively small projections that some our snails sport are preforming the same job that those weirdly distorted&nbsp;</span><i style="background-color: white; text-align: center;">Opisthostoma</i><span style="background-color: white; text-align: center;">&nbsp;shells serve.</span></div>
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</div>David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-69365566181607431472012-07-22T17:30:00.000+12:002012-07-22T18:01:54.927+12:00Sunday Spinelessness - New Zealand microsnailsWhen I tell people I study snails for a living I get one of two replies. There's either some version of the "joke" that goes "that must be slow-going" or "sounds action packed", or there's "oh, you mean those giant killer ones we saw when we went tramping?". I guess the joke is funny enough, but I want to make it clear that those<a href="http://sciblogs.co.nz/the-atavism/2011/06/26/sunday-spinelessness-snails-can-be-speedy-too/"> giant killer snails from&nbsp;the&nbsp;family Rhytidae</a>, cool as they might be, are not the most interesting land snails in New Zealand.<br />
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The local land snail fauna displays a pattern that is quite common for New Zealand animals - we have a very large number of species but those species are drawn from relatively few taxonomic&nbsp;families. Since taxonomic groups reflect the evolutionary history of the species they contain, that pattern most likely arises because New Zealand is (a) quite hard to get to, so few would-be&nbsp;colonists&nbsp;make it here and (b) full of ecological niches and<span style="background-color: white;">&nbsp;geographic pockets that can drive the formation of new species. In total, there are are probably about 1200&nbsp;native land snail species in New Zealand - about ten times the number found in Great Britain, which is&nbsp;approximately&nbsp;the same size. That diversity extends to the finest scales - individual sites in native forest might have as many as 60 species sharing the habitat. New&nbsp;Zealand&nbsp;forests probably have the most diverse land snails assemblages in the world (although tropical ecologists, who generally hold that&nbsp;diversity&nbsp;in terrestrial habitats almost invariably increases as you approach the equator, have argued against this conclusion).</span><br />
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<span style="background-color: white;">You may now be asking why, if this land snail fauna is so diverse, have you never seen a native snail. Well, you've probably walked past thousands of them without noticing. Most of our native land snail species are from the families Punctidae and Charopidae, groups that are sometimes given the common name "dot snails". Meembers of these&nbsp;families&nbsp;are usually smaller than 5 mm across the shell, and are restricted to native forest and in particular to leaf litter. But in native forests, where there's leaf litter there's snails. Grab a handful of leaves, or pull up a log and you're likely to find a few tiny flat-spired&nbsp;snails going about their business.&nbsp;Hell, down here in Dunedin you can even find&nbsp;<a href="http://sciblogs.co.nz/the-atavism/2011/04/24/sunday-spinelessness-incertae-sedis/">charopids living under tree-fuschia in a suburban garden</a>.</span><br />
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<span style="background-color: white;">Like so many native invertebrates, we know very little about our land snails. Lots of people have&nbsp;dedicated substantial parts of their lives to documenting and describing the diversity of these creatures, but even so we don't have a clear understanding of how the native species relate to each other or to their relatives in the rest of the world, or even where one species starts and another ends. Without such a basic understanding, its very hard to ask evolutionary and ecological questions about these species, so for now we remain largely ignorant of the forces that have created the New Zealand land snail fauna.</span><br />
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<span style="background-color: white;">For the time being I can tell you that&nbsp;<a href="http://sciblogs.co.nz/the-atavism/2012/03/25/sunday-spinelessness-looking-into-the-sprial/">a lot of them are really quite&nbsp;beautiful.</a>&nbsp;Since most people don't have handy access to a microscope to see these critters, I thought I would share a few photos from this largely neglected group over the next few weeks. The 2D photographs, with the relatively fine depth of field, don't quite record the beauty of these 3D shells, but I hope it's at least a window into the diversity of these snails.</span><br />
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<span style="background-color: white;">&nbsp;</span><span style="background-color: white;">Let's start with a snail that is very common in Dunedin parks and forests. This is a species from the genus&nbsp;</span><i>Cavellia </i><span style="background-color: white;">(the strong, sine-shaped ribs being the giveaway)</span><span style="background-color: white;">&nbsp;but I won't be able to place it to species until a new review of that genus is published.&nbsp;</span><br />
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<img src="http://lh4.googleusercontent.com/-i5fmtyfx4uo/UAt8z5i67zI/AAAAAAAAR-E/EN_2BawlYSg/s724/dud-16.jpg" width="650px" /><br />
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This particular shell is from an immature specimen, and is about 2mm across. When flipped, you can see an open umbilicus that lets you see straight through to the apex of the shell.<br />
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<br />David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com1tag:blogger.com,1999:blog-4718577088343779246.post-8148427076011037402012-07-11T12:48:00.001+12:002012-07-11T12:49:47.182+12:00You can't ban redheaded spermIt's the first week of semester two down here at Otago, which means I will helping with undergraduate labs for the first time this year. I suspect most students end up not liking me all that much, because I find my self teaching in the parts of the genetics program that undergrads like the least. Population genetics, as the name suggests, is the study of the way genes behave in populations, and in many ways its the base from which our understanding of evolution is built. So it's important, but it's also pretty mathsy.<br />
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<span style="background-color: white;">It seems quite a few students have planned their high school and unversity careers in the hope that studying biology meant that&nbsp;could&nbsp;leave maths behind. So, when they are confronted with "</span><b style="background-color: white;">p<sup>2</sup> + 2pq + q<sup>2</sup> = 1</b><span style="background-color: white;">" and asked to do something with it, they are unhappy.</span><br />
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That particular formula is for something called the <a href="http://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle">Hardy-Weinberg equilibrium</a>&nbsp;and a&nbsp;significant&nbsp;proportion of students roll their eyes and slump their&nbsp;shoulders&nbsp;when you tell them they are going to need to use it for a problem. They think its arbitrary and irrelevant to anything the least bit important, and what's more it looks a little like it's already solved. So, I'm always looking for ways to convince people that Hardy-Weingberg isn't just simple, but actually intuitive and important. So here's my attempt to explain why knowing a little population genetics is helpful.<br />
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You may remember last year &nbsp;<a href="http://www.telegraph.co.uk/news/worldnews/europe/denmark/8768598/Sperm-bank-turns-down-redheads.html">a Danish sperm bank had started turning away would-be&nbsp;donors&nbsp;with red hair</a>, since there is little demand for sperm that might contribute to the creation of a readhead. It turns out, if you know a little bit about population genetics you can see that policy will have little effect on the number of red heads&nbsp;the&nbsp;sperm bank helps to bring into the world.<br />
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Hair&nbsp;colour&nbsp;is partially controlled by a gene called <a href="http://en.wikipedia.org/wiki/Melanocortin_1_receptor">MC1R</a>. There are different versions of MC1R floating around in human populations, and one of them has a mutation that stops melanin (a&nbsp;dark pigment)&nbsp; passing into hairs as they grow. Geneticists call different versions of a gene "alleles", so we'll call this flavour of MC1R the "red hair allele" and give it the symbol <i>r</i>.As I'm sure you know, you have two copies of most of your genes, one inherited from your mother and the other from your father. Red hair is a recessive trait, which means in order to have red hair both of your copies of MC1R need to be the <i>r</i> allele: if you have one or two copies&nbsp;of the "normal" MC1R allele (which we'll call "R") you have some pigment passing into your hair and it will be another colour. We call the total genetic make-up of a person their "genotype", and their&nbsp;physical&nbsp;characteristics their "phenotype", so here's a table showing the genotypes and the phenotypes we're talking about in this post:<br />
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<tr><td><b>Genotype&nbsp;</b></td><td><div style="text-align: center;">
<i>r</i>/<i>r</i></div>
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<i>r</i>/<i>R</i></div>
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<i>R</i>/<i>R</i></div>
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<b>Phenotype (hair colour)</b></div>
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<span class="Apple-style-span" style="background-color: #ea9999;">Red Hair</span></div>
</td><td>Not Red Hair</td><td>Not Red Hair</td></tr>
</tbody></table>
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I know there are a lot of technical terms there (<a href="http://blogs.discovermagazine.com/loom/2009/11/30/the-index-of-banned-words-the-continually-updated-edition/">Carl Zimmer will not be happy.</a>..), but we do need to be precise when we talk about genetics because, strange as it may seem, there isn't a single&nbsp;definition&nbsp;of the word gene. Once you've got your head around the terms, it's all pretty straight forward: you need two copies of the <i>r</i> allele to have red hair.&nbsp;Think what this means for the Danish sperm bank though. Turning away red headed sperm&nbsp;donors doesn't turn away red headed sperm since there will still be "carriers" with only one copy of <i>r</i> (and, thus, non-red hair) donating sperm and half of <i>those</i>&nbsp;sperm will be "red headed sperm".<br />
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How big a problem is this likely to be? First we need to work how common the <i>r</i> allele is, and we can use the frequency of redheads to find that.&nbsp;By long tradition, the frequency of a&nbsp;recessive&nbsp;allele is denoted by "<b>q</b>", so, in a population where one quarter of the alleles are <i>r</i> we'd say <b>q</b> = 0.25. We know that in order to have red hair you need both your copies of the MC1R gene to be the <i>r</i> allele and that you inherit each allele&nbsp;separately. When probabilities are independant we can mutiply them, so the chace someone in this population is a redhead is&nbsp;<b>q</b>&nbsp;x&nbsp;<b>q</b>&nbsp;=&nbsp;<b>q<sup>2 &nbsp;</sup></b>= 0.06 .Following the same logic, the frequency of the <i>R</i>/<i>R</i>&nbsp;genotype must be the frequency of <i>R</i>&nbsp;squared (by convention, the frequency of a dominant allele is called "<b>p</b>", so that's <b>p<sup>2</sup></b>).<br />
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Knowing this relationship, we can work backwards and find the frequency of <i>r</i> if we know the proportion of redheads in a population. In most of Northern Europe, about 4% (0.04) of the populaiton are redheads so&nbsp;&nbsp;<b>q<sup>2</sup>&nbsp;= 0.04</b> and <b>q = √0.04 = 0.2</b>. As you can see, red hair genes can be a lot more common than redheads:<br />
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<img src="https://lh5.googleusercontent.com/-ay7IvnBXgL4/To_PLhKH-5I/AAAAAAAARns/QE50UvF7hGE/s550/alleles.png" />
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To understand how the sperm bank's policy will we work, we need to know about those 'carriers' with the mixed genotypes (called "heterozygotes" by genetics geeks). It doesn't matter which order your genes come in, so the&nbsp;probability&nbsp;of being a carrier in the population above will be the chance of getting an <i>R</i> then and <i>r</i> (<b>p x q</b>) plus the chance of getting and <i>r</i> followed by an <i>R</i> (<b>q x p</b>). You can simplify that to<b> 2pq</b>. You might&nbsp;recognize&nbsp;that term, because with it we've&nbsp;rediscovered&nbsp;the one in the first paragraph&nbsp;"<b>p<sup>2</sup>&nbsp;+ 2pq + q<sup>2</sup>&nbsp;= 1</b>". The Hardy-Weinberg&nbsp;equation&nbsp;is just away of moving from allele frequencies to genotype frequencies (or the other way around) and it's based on some very simple observations about the way populations work. We saw that in a population with&nbsp;&nbsp;4% redheads you get <b>q = 0.2</b>, so <b>p=0.8</b> and <b>2pq = 2 x 0.2 x 0.8 = 0.32</b>. Almost a third of the population are carriers, and that's eight times the number of redheads! While the frequency of the red hair allele is low, only a small proportion of the red haired alleles in a population will actually in red&nbsp;haired&nbsp;people:<br />
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<img src="https://lh4.googleusercontent.com/-EAneaFZPBaM/To_PL0ptz5I/AAAAAAAARn0/E03brj2GQEg/s571/hets.png" />
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That's why the sperm banks policy, while prefectly sensible if there really is no demand for sperm from redheads, will do little prevent the creation of&nbsp;red-headed&nbsp;babies. &nbsp;In the typical case, where 4% of the population are redheads the probability that a donated sperm carries the <i>r</i> allele only moves from 20% to 17% when you exclude red haired donors<br />
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It's easy to calculate how the policy would work in populations with more or less redheads:<br />
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<img src="https://lh4.googleusercontent.com/-tLTdHofB6pQ/To_PL8eFY4I/AAAAAAAARrA/yR9jFtsU8-c/s557/policy.png" />
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So, that annoying equation we make the undergrads learn actually tells us something about the world. Obviously, the example I've talked about here is a pretty silly one, but the basic ideas we've discovered above can help us understand some important ideas. Like why genes that cause debilitating diseases aren't completely removed by natural selection, and why inbreeding is a bad idea.<br />
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A lot of rare diseases are caused by&nbsp;recessive&nbsp;alleles. They remain rare for the obvious reason that people with such diseases are unlikely to pass on their genes. But they remain present in populations because, as we've found, once recessive alleles get rare the&nbsp;overwhelming&nbsp;majority of them are found in carriers. In this way, rare recessive alleles are seldom exposed to selection so they stick around for a long time.*<br />
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Because disease causing genes stick around in populations, there is a pretty good chance that you carry a few alleles that would cause a debilitating disease in someone who had two copies of them. The same applies to anyone you might be hoping to have children with. Thankfully, its very unlikely that your prospective mate with have disease-causing alleles for the&nbsp;<i>same</i>&nbsp;genes that you do. That is, as long as you look beyond the family tree when you look for a mate. If you have a child with someone who is closely related to you, you will have each inherited some of your genes from the same source, which increases the chances you share disease alleles.<br />
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*In fact, they often reach a point called "mutation-selection balance" in which the frequency of the allele remains static because new mutations re-create the allele as quickly as&nbsp;selection&nbsp;removes it. JBS Haldane was the first person to notice this, and he used his theory to create <a href="http://sciblogs.co.nz/the-atavism/2009/09/07/i-told-you-youre-all-mutants/">a very accurate estimate of the human mutation rate</a>&nbsp;well before we knew what genes were made of!David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com3tag:blogger.com,1999:blog-4718577088343779246.post-16258702961523684372012-07-08T21:51:00.000+12:002012-07-08T21:51:44.681+12:00Sunday Spinelessness - Cuttlefish in drag deceive their rivalsOne awesome mollusc&nbsp;deserves&nbsp;another, so let's follow up<a href="http://sciblogs.co.nz/the-atavism/2012/07/01/sunday-spinelessness-the-other-mollusc-shell/"> last weeks octopus post</a> with one on that group's close relatives the cuttlefish.<br />
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Cuttlefish are relatively small (the largest grow to 50cm) squid-like cephalopods that&nbsp;present a nice soft and&nbsp;digestible&nbsp;meal to predatory fish and marine mammals. Having lost the shell that most molluscs use to protect themselves cuttlefish have had to develop other defences. Most strikingly, cuttlefish are masters of&nbsp;<span style="background-color: white;">camouflage</span><br />
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The deceptive patterns that cuttlefish put on come from their remarkable skin, and are controlled by a pretty impressive nervous system. The skin is covered in cells called chromatophores which contain granules of pigment. When a cuttlefish decides it's time to&nbsp;disappear it looks around its surroundings and, with the aid of nerves that lead from the brain to the the skin, stretch and twist the chromoatophores&nbsp;&nbsp;on the skin's surface in such as way as to change the colour of their cells, and&nbsp;ultimately&nbsp;their whole bodies.&nbsp;</div>
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That impressive trick is principally used for&nbsp;camouflage, but cuttlefish and also use their skin as a sort of billboard to signal to other&nbsp;members&nbsp;of their own species, and even put on a strobing light show (possibly used to startle their own prey):<br />
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Just this week, researchers have reported evidence for a other trick that cuttlefish can pull off. When males of the Austrian Mourning Cuttlefish (<i>Sepia plangon</i>) see a female they put on a show, producing striped patterns that evidently impress the female. But these animals form male-dominated groups, and rival males often interrupt would-be woo-ers &nbsp;in mid-display. So, when they spy a receptive female, males want to put on their flamboyant show for her to judge, but also want to make sure they don't&nbsp;attract&nbsp;the attention of rival males that might want to spoil the party. The male Mourning Cuttlefish's answer to this problem? Using only half of his body to put on the female-impressing show, and throwing would-be spoilers off the scent by&nbsp;mimicking&nbsp;a female with the other half.<br />
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This gender-splitting &nbsp;tactic seems to be pretty common. In&nbsp;aquarium&nbsp;experiments about 40% of males would &nbsp;attempt the&nbsp;deceptive&nbsp;signal&nbsp;when they were displaying in the presence of a rival. Just as the&nbsp;cuttlefish camouflage&nbsp;response requires information from the physical environment, the gender-splitting trick is influenced by what the male can learn of the social environment. If more than one female is&nbsp;available&nbsp;the male will display to both &nbsp;without bothering to hide his intentions for observers (probably because working out an angle from which he could excite two females while staying under the radar is just not possible). Likewise, if more than one rival male is about that don't bother with the deception - since it wouldn't be possible to maintain the illusion for two rivals viewing from&nbsp;different&nbsp;positions.<br />
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Brown, Garwood &amp; Williamson (In press) It pays to cheat: tactical deception in a cephalopod social signalling system. <span style="background-color: white;"><i>Biology Letters</i></span><span style="background-color: white;">. </span><a href="http://dx.doi.org/10.1098/rsbl.2012.0435" style="background-color: white;">http://dx.doi.org/10.1098/rsbl.2012.0435w</a><br />
<br />David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0tag:blogger.com,1999:blog-4718577088343779246.post-78649782405595032752012-07-01T21:31:00.001+12:002012-07-01T21:35:53.616+12:00Sunday Spinelessness - The other mollusc shell<div style="text-align: left;">
Here's a really cool animal, a&nbsp;female&nbsp;<a href="http://en.wikipedia.org/wiki/Argonaut_(animal)">argonaut</a>&nbsp;(sometimes called a paper nautilus):</div>
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<span style="background-color: white;">It may not be immediately obvious from the photo, but a</span><span style="background-color: white;">rgonauts</span><span style="background-color: white;">&nbsp;are octopuses. Strange&nbsp;octopuses,&nbsp;because&nbsp;the seven species that make up the family Argonautidea are among a handful of octopuses that are capable of swimming through the water column (rather than hanging out on the&nbsp;ocean&nbsp;floor) and they are the only octopuses that fashion themselves a shell.&nbsp;</span></div>
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The argonaut shell has been a topic of consideration, confusion and conjecture for biologists for a long time. Only females produce the shell. Male argonauts are tiny (about a tenth of the size of the female) and only really serve as sperm donors (in fact, they donate an entire&nbsp;sperm-transferring organ, called the&nbsp;<a href="http://en.wikipedia.org/wiki/Hectocotylus">hectocotylus</a><span style="background-color: white;">). Once mated, a female argonaut starts producing her shell and lays her eggs in its base. This behaviour has lead some biologists to conclude the shell's primary function is to act as an egg case. &nbsp;We now know that shell is also used to help the argonaut maintain its position in the water column. By propelling herself to the surface and rocking back and forth an argonaut can introduce an air bubble into her shell. While she's near the surface that air bubble will make her&nbsp;buoyant, but by diving downwards she can reach a point where the increasing water pressure (which compresses the air bubble, decreasing its buoyancy) cancels out the&nbsp;buoyant effect, letter her float in the&nbsp;water colum. At that point she's free to swim about in two dimensions without having to maintain her vertical position.</span></div>
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You can watch this remarkable&nbsp;behaviour&nbsp;&nbsp;here:</div>
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I don't want to talk too much more about the purpose of the argonaut shell, partly because it has already been well covered.&nbsp;<span style="background-color: white;">Ed Yong wrote&nbsp;</span><a href="http://blogs.discovermagazine.com/notrocketscience/2010/05/18/the-argonaut-%E2%80%93-an-octopus-that-creates-its-own-ballast-tank/" style="background-color: white;">a&nbsp;predicably&nbsp;clear and&nbsp;interesting post</a><span style="background-color: white;">&nbsp;</span><span style="background-color: white;">on the research which uncovered it (which also produced an interesting comments thread) and the lead researcher, Julian Finn from&nbsp;Museum&nbsp;Victoria in Australia, also discussed his work <a href="http://museumvictoria.com.au/about/mv-news/2010/argonaut-buoyancy/argonaut-video/">in a really great video</a>.</span><br />
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<span style="background-color: white;">Instead, I want to talk about the <i>origin</i> of the argonaut&nbsp;shell. Octopuses are&nbsp;molluscs, part of a group of soft-bodied animals that includes clams and&nbsp;mussels&nbsp;and snails. Most molluscs have shells. In fact,&nbsp;despite&nbsp;being&nbsp;</span><span style="background-color: white;">arugably the most&nbsp;morphologically&nbsp;diverse of the 35 animal phyla, only a few small groups of molluscs don't contain at least some species that produce shells. The easiest way to explain the presence of shells in so many different molluscan groups is to&nbsp;hypothesize&nbsp;that the last common ancestor of all molluscs had a shell, and most of that ur-mollsuc's&nbsp;descendants&nbsp;have&nbsp;retained&nbsp;this organ.&nbsp;</span><br />
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In evolutionary biology we call traits that are shared between organisms as a result of their shared evolutionary history "homologies". Homologous traits are often compared with "analgous" ones, parts of organisms that are similar as the result of&nbsp;independent&nbsp;innovations&nbsp;in different evolutionary lineages. We can illustrate the concept using a bat's wing as an example. The forelimbs of bats and whale are made up of the same bones, despite the fact that whales swim and bats fly. That's because bats and whales are both mammals, and they inherited their forelimb bones from a common ancestor before each group radically&nbsp;repurposed their limbs. On the other hand, despite the fact that both bats and <a href="http://en.wikipedia.org/wiki/Plecoptera">stoneflies</a> fly, the insect wing and the bat wing are&nbsp;separate&nbsp;evolutionary inventions and not something the two groups share as a result of shared evolutionary history:<br />
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The protective shells of snails and clams are homologous to each other, and to the internatilized shells that some squids use to stay afloat. But the argonaut shell is something entirely different. The argonaut shell is made of calcite, where most molluscan shells are argonite. Moreover, the minerals that make up the argonaut shell are extruded from the octopuses tentacles, where other molluscs have an organ&nbsp;called&nbsp;the mantle that they use to produce their shell.&nbsp;</div>
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The fact the argonaut shell is made of different stuff than other molluscan shells, and with the aid of &nbsp;a&nbsp;different&nbsp;organ, suggests it is a unique evolutionary innovation. So how did shells evolve twice within the molluscs? I can't provide you with a&nbsp;definitive&nbsp;answer, but I do like one (only slightly crazy) speculation. Earth's oceans used to be dominated by another group of shelled molluscs called <a href="http://en.wikipedia.org/wiki/Ammonoidea">ammonites</a>. <a href="http://en.wikipedia.org/wiki/Adolf_Naef">Adolf&nbsp;Naef</a>&nbsp;pointed out that argonaut shells are very similar to some ammonite shells, and suggested the ancestors of ammonites might have laid their eggs in discarded ammonite shells (some modern octopuses certainly spend time hanging out in mollusc shells). Naef suggested ancestral argonauts might then have&nbsp;acquired&nbsp;the ability to repair broken shells (developing the mineral secreting organs on their tenticles) and finally to create their own.&nbsp;</div>
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It's a pretty out-there sort of an idea, and I don't know how you&nbsp;could&nbsp;actually test it. But wouldn't it be cool if the ammonite shell was still being dutifully copied every day, 65 million years after the last ammonite died?</div>
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<br /></div>David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com6tag:blogger.com,1999:blog-4718577088343779246.post-83446827755986971472012-06-17T20:28:00.000+12:002012-06-17T20:28:43.498+12:00Sunday Spineless - How some snails became red-bloodedHere's something cool that I've meaning to write&nbsp;about&nbsp;for a long time. A native&nbsp;<i>Powelliphanta</i>&nbsp;land snail with an apparently pigment-less foot and head:<br />
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That snail (<a href="http://sciblogs.co.nz/the-atavism/2011/06/26/sunday-spinelessness-snails-can-be-speedy-too/">a close relative of speedy carnivore featured here</a>) popped up in Kahurangi National Park at the end of last year. Apart from just being kind of cool, the un-pigmented individual is interesting for a geneticist that studies land snails. For the most part, dark pigmentation in snails results form melanin &nbsp;(which is perhaps the most common pigment in the animal world). That's true for pigmentation of the shell as well as the animal that caries it around. As you can see, this snail has normal pigmentation on its shell, so clearly its still able to make melanin. The genetic mutation (or&nbsp;developmental&nbsp;defect) that has left this snail white hasn't broken the genes for pigmentation, just the mechanism that moves that pigment around the body wall of the snail.<br />
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The ghost <i>Powelliphanta </i>is a pretty cool snail, but there's actually an albino snail that's even more interesting. Every now and again a truly albino individual of the freshwater snail&nbsp;<i>Biomphalaria glabrata </i>pops up. Looking at these mutants we can learn something about the&nbsp;evolutionary&nbsp;history of the these snails:<br />
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<i style="font-size: 13px;">Photo is&nbsp;<a href="http://creativecommons.org/licenses/by-sa/3.0/deed.en">CC 2.5</a>&nbsp;and comes from&nbsp;</i><i style="font-size: 13px;">Lewis FA, Liang Y-s, Raghavan N, Knight M et al in&nbsp;</i><i style="font-size: 13px;"><a href="http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0000267">PLoS Tropical Diseases</a></i><br />
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Free from the pigments that would usually make shell opaque we can see the feature that sets&nbsp;<i>Biomphalaria </i>and other species form the family <a href="http://en.wikipedia.org/wiki/Planorbidae">Planorbidae</a>&nbsp;(ramshorn snails) apart from every other snail. The planorbids are&nbsp;the&nbsp;only red-blooded snails on earth. So why are these snails so different?<br />
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As we all know, in order to live animals need to get oxygen from their environment into their bodies.&nbsp;For small animals this doesn't represent a huge problem. Oxygen will flow form areas of high partial pressure (a concept analgous to concentration, but accounting for some of the weird ways gasses behave) to areas in which Oxygen is being used up. So, for instance, most insects pull air directly into their bodies with a set of open tubes (called&nbsp;<a href="http://en.wikipedia.org/wiki/Invertebrate_trachea">tracheae</a>). Once the air makes it into those tubes oxygen will passively diffuse into the insect's tissues.<br />
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Big animals have a much bigger problem*. Not only do larger animals need much more oxygen to fuel their bodies, they also have to actively transport that Oxygen because the distances it is required to travel can't be&nbsp;achieved&nbsp;by passive&nbsp;diffusion. Lungs and gills are both organs dedicated to pumping more oxygen into animal bodies, and many &nbsp;animals use blood, and special proteins&nbsp;dissolved&nbsp;in blood, to move oxygen about.<br />
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In vertebrates the oxygen-carrying protein is called hemoglobin. Very simply, a&nbsp;hemoglobin molecule is &nbsp; a cage used to hold iron atoms in such a way that they will bind to an oxygen atom. The iron containing group in the hemoglobin protein (called heme)&nbsp;gives our blood its red colour and its hemoglobin circulating through that snail's body that makes it red.<br />
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<small><i>Heart of Steel is Julian Voss Andreae's sculpture based on the structure of hemoglobin proteins. Pleasingly, the weathering process depicted across &nbsp;these photos is the result of iron molecules in the steel sculpture binding with oxygen - the very process that underlies the function of hemoglobin. Photo is <a href="http://creativecommons.org/licenses/by-sa/3.0/deed.en">CC 3.0</a> care of the artist.</i></small></div>
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As with every problem life faces, invertebrates have come up with many more interesting ways to move oxygen around than their spined relatives. Annelids (earthworms and their kin), brachiapods and spoon worms have a whole set of iron-containing proteins to do the job. Even more interestingly, molluscs and some&nbsp;arthropods&nbsp;have a protein that uses Copper rather than Iron atoms to co-ordinate an oxygen molecule. This molecule, called hemocyanin, takes on a green-ish blue hue when oxygen binds to it and changes its conformation.<br />
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Most snails get through life fine with&nbsp;hemocyanin as the only oxygen-carrying molecule in their blood, so why have&nbsp;<i>Biomphalaria </i>and their cousins become red-blooded? Part of the reasons lies in their lifestyle. Planorbid snails breath with lungs (which only work in air) but live underwater. If you make your living by holding your breath while diving then you really want to have some way of holding on to as much of the oxygen you get form each breath for as long as possible. It seems that&nbsp;<i>Biomphalaria </i>hemoglobin is more efficient at using the oxygen stored&nbsp;&nbsp;in lungs while diving than any hemocyanin could be.<br />
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It's all well talking about <i>why </i>an animal might have evolved a particular trait. But in evolutionary biology it's generally much more intresting to try and work out <i>how.</i><i>&nbsp;</i>How does an air-breathing snail make its own hemoglobin from scratch? A team lead by&nbsp;<a href="http://www.staff.uni-mainz.de/lieb/">Bernhard Lieb</a> asked just that question a few years ago, and found the answer:&nbsp;<i>Biomphalaria </i>hemoglobin was made by&nbsp;cobbling&nbsp;together parts of existing proteins. When Lieb <i>et al</i>&nbsp;(2006, doi:&nbsp;<a href="http://10.0.4.49/pnas.0601861103">10.1073/pnas.0601861103</a>) isolated hemoglobin from red-blooded snails they found it was made up of two different components (called peptides), each of which has 13 different sub-components (called <a href="http://en.wikipedia.org/wiki/Protein_domain">domains</a>). When the team compared the sequence of those peptides and their domains to other molluscan proteins they found similarties between the hemoglobin sequences and another iron-containing protein called myoglobin.<br />
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Myoglobin is a small molecule that is usually restricted to muscles where is acts as a store of Oxygen (in snails, myoglobin is most commonly found in the muscles that drive the radula, the rasp like organ used to break down food). The&nbsp;<i>Biomphalaria&nbsp;</i>hemoglobin&nbsp;sequences are more closely related to each other than they are to myoglobins from any other species. This pattern suggests the sequences that make up the snail hemoglobin descend from a single common ancestor. Subsequent changes to each of these&nbsp;descendants&nbsp;have allowed the descendants proteins to group together and&nbsp;become&nbsp;"super myoglobins" capable of transporting oxygen through the body.<br />
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*The huge number of ways size matters in biology were wonderfully explained by JBS Haldane. I'd reproduce the most famous passage here, <a href="http://irl.cs.ucla.edu/papers/right-size.html">but it's probably even better if you discover it by yourself.</a><br />
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<br />David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com2tag:blogger.com,1999:blog-4718577088343779246.post-67003606516240510462012-06-03T19:32:00.000+12:002012-06-03T19:32:16.275+12:00Sunday Spinelessness - Nothing to see here<div style="text-align: left;">
I'm off to the&nbsp;<a href="http://www.royalsociety.org.nz/events/2012-transit-of-venus-forum-lifting-our-horizon/">Transit&nbsp;of Venus Forum</a>&nbsp;next week. I'm looking forward to meeting all sorts of clever and interesting people (and escaping&nbsp;<a href="http://www.stuff.co.nz/the-press/news/7037732/Snow-to-arrive-in-south-this-week">the coming snow</a>), but travelling and conferring won't leave much time for a few projects I really need to work on. So, today's blog post is going to have to be squeezed down to its smallest&nbsp;possible&nbsp;form&nbsp;(a queen ant that dropped in to read an early draft of my thesis last spring):</div>
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<br /></div>David Winterhttp://www.blogger.com/profile/09704684760112027351noreply@blogger.com0